Imaging purple membranes in aqueous solutions at sub-nanometer resolution by atomic force microscopy

Increased imaging speed and force sensitivity for bio-applications with small cantilevers using a conventional AFM setup

In this study, we demonstrate the increased performance in speed and sensitivity achieved by the use of small AFM cantilevers on a standard AFM system. For this, small rectangular silicon oxynitride cantilevers were utilized to arrive at faster atomic force microscopy (AFM) imaging times and more sensitive molecular recognition force spectroscopy (MRFS) experiments. The cantilevers we used had lengths between 13 and 46 μm, a width of about 11 μm, and a thickness between 150 and 600 nm. They were coated with chromium and gold on the backside for a better laser reflection. We characterized these small cantilevers through their frequency spectrum and with electron microscopy. Due to their small size and high resonance frequency we were able to increase the imaging speed by a factor of 10 without any loss in resolution for images from several μm scansize down to the nanometer scale. This was shown on bacterial surface layers (s-layer) with tapping mode under aqueous, near physiological conditions and on nuclear membranes in contact mode in ambient environment. In addition, we showed that single molecular forces can be measured with an up to 5 times higher force sensitivity in comparison to conventional cantilevers with similar spring constants.

Microbial cells analysis by atomic force microscopy

Unraveling the structure of microbial cells is a major challenge in current microbiology and offers exciting prospects in biomedicine. Atomic force microscopy (AFM) appears as a powerful method to image the surface ultrastructure of live cells under physiological conditions and allows real-time imaging to follow dynamic processes such as cell growth, and division and effects of drugs and chemicals. The following chapter introduces different methods of sample preparation to gain insights into the microbial cell organization. Successful strategies to immobilize microorganisms, including physical entrapment and chemical attachment, are described. This step is a key step and a prerequisite of any analysis and persists as an important limitation to the application of AFM to microbiology due to the wide diversity of microorganisms. Finally, some applications are depicted which underlie the ability of AFM to explore living microbes with unprecedented resolution.

Investigating fibrillar aggregates of Tau protein by atomic force microscopy

Atomic force microscopy (AFM) has been used in numerous studies to visualize and analyze the structure and conformation of biological samples, from single molecules to biopolymers to cells. The possibility to analyze native samples without fixation, staining and in physiological buffer conditions, combined with the sub-nanometer resolution, makes AFM a versatile tool for the analysis of protein aggregation and amyloid structures. Here, we describe the application of AFM to study fibrillar Tau protein aggregates.

Molecular cooperativity of drebrin1-300 binding and structural remodeling of F-actin

Drebrin A, an actin-binding protein, is a key regulatory element in synaptic plasticity of neuronal dendrites. Understanding how drebrin binds and remodels F-actin is important for a functional analysis of their interactions. Conventionally, molecular models for protein-protein interactions use binding parameters derived from bulk solution measurements with limited spatial resolution, and the inherent assumption of homogeneous binding sites. In the case of actin filaments, their structural and dynamic states-as well as local changes in those states-may influence their binding parameters and interaction cooperativity. Here, we probed the structural remodeling of single actin filaments and the binding cooperativity of DrebrinA(1-300) -F-actin using AFM imaging. We show direct evidence of DrebrinA(1-300)-induced cooperative changes in the helical structure of F-actin and observe the binding cooperativity of drebrin to F-actin with nanometer resolution. The data confirm at the in vitro molecular level that variations in the F-actin helical structure can be modulated by cooperative binding of actin-binding proteins.

Microcantilevers and organic transistors: two promising classes of label-free biosensing devices which can be integrated in electronic circuits

Most of the success of electronic devices fabricated to actively interact with a biological environment relies on the proper choice of materials and efficient engineering of surfaces and interfaces. Organic materials have proved to be among the best candidates for this aim owing to many properties, such as the synthesis tunability, processing, softness and self-assembling ability, which allow them to form surfaces that are compatible with biological tissues. This review reports some research results obtained in the development of devices which exploit organic materials' properties in order to detect biologically significant molecules as well as to trigger/capture signals from the biological environment. Among the many investigated sensing devices, organic field-effect transistors (OFETs), organic electrochemical transistors (OECTs) and microcantilevers (MCLs) have been chosen. The main factors motivating this choice are their label-free detection approach, which is particularly important when addressing complex biological processes, as well as the possibility to integrate them in an electronic circuit. Particular attention is paid to the design and realization of biocompatible surfaces which can be employed in the recognition of pertinent molecules as well as to the research of new materials, both natural and inspired by nature, as a first approach to environmentally friendly electronics.

Resolving structure and mechanical properties at the nanoscale of viruses with frequency modulation atomic force microscopy

Structural Biology (SB) techniques are particularly successful in solving virus structures. Taking advantage of the symmetries, a heavy averaging on the data of a large number of specimens, results in an accurate determination of the structure of the sample. However, these techniques do not provide true single molecule information of viruses in physiological conditions. To answer many fundamental questions about the quickly expanding physical virology it is important to develop techniques with the capability to reach nanometer scale resolution on both structure and physical properties of individual molecules in physiological conditions. Atomic force microscopy (AFM) fulfills these requirements providing images of individual virus particles under physiological conditions, along with the characterization of a variety of properties including local adhesion and elasticity. Using conventional AFM modes is easy to obtain molecular resolved images on flat samples, such as the purple membrane, or large viruses as the Giant Mimivirus. On the contrary, small virus particles (25-50 nm) cannot be easily imaged. In this work we present Frequency Modulation atomic force microscopy (FM-AFM) working in physiological conditions as an accurate and powerful technique to study virus particles. Our interpretation of the so called "dissipation channel" in terms of mechanical properties allows us to provide maps where the local stiffness of the virus particles are resolved with nanometer resolution. FM-AFM can be considered as a non invasive technique since, as we demonstrate in our experiments, we are able to sense forces down to 20 pN. The methodology reported here is of general interest since it can be applied to a large number of biological samples. In particular, the importance of mechanical interactions is a hot topic in different aspects of biotechnology ranging from protein folding to stem cells differentiation where conventional AFM modes are already being used.

Heteroepitaxial streptavidin nanocrystals reveal critical role of proton "fingers" and subsurface atoms in determining adsorbed protein orientation

Characterization of noncovalent interactions between nanometer-sized structures, such as proteins, and solid surfaces is a subject of intense interest of late owing to the rapid development of numerous solid materials for medical and technological applications. Yet the rational design of these surfaces to promote the adsorption of specific nanoscale complexes is hindered by a lack of an understanding of the noncovalent interactions between nanostructures and solid surfaces. Here we take advantage of the unexpected observation of two-dimensional nanocrystals of streptavidin on muscovite mica to provide details of the streptavidin-mica interface. Analysis of atomic force microscopic images together with structural modeling identifies six positively charged residues whose terminal amine locations match the positions of the single atom-sized anionic cavities in the basal mica surface to within 1 Å. Moreover, we find that the streptavidin crystallites are oriented only along a single direction on this surface and not in either of three different directions as they must be if the protein interacted solely with the 3-fold symmetric basal surface atoms. Hence, this broken symmetry indicates that the terminal amine protons must also interact directly with the subsurface hydroxide atoms that line the bottom of these anionic cavities and generate only a single axis of symmetry. Thus, in total, these results reveal that subsurface atoms can have a significant influence on protein adsorption and orientation and identify the insertion of proton "fingers" as a means by which proteins may generally interact with solid surfaces.

Submolecular-scale imaging of α-helices and C-terminal domains of tubulins by frequency modulation atomic force microscopy in liquid

In this study, we directly imaged subnanometer-scale structures of tubulins by performing frequency modulation atomic force microscopy (FM-AFM) in liquid. Individual α-helices at the surface of a tubulin protofilament were imaged as periodic corrugations with a spacing of 0.53 nm, which corresponds to the common pitch of an α-helix backbone (0.54 nm). The identification of individual α-helices allowed us to determine the orientation of the deposited tubulin protofilament. As a result, C-terminal domains of tubulins were identified as protrusions with a height of 0.4 nm from the surface of the tubulin. The imaging mechanism for the observed subnanometer-scale contrasts is discussed in relation to the possible structures of the C-terminal domains. Because the C-terminal domains are chemically modified to regulate the interactions between tubulins and other biomolecules (e.g., motor proteins and microtubule-associated proteins), detailed structural information on individual C-terminal domains is valuable for understanding such regulation mechanisms. The results obtained in this study demonstrate that FM-AFM is capable of visualizing the structural variation of tubulins with subnanometer resolution. This is an important first step toward using FM-AFM to analyze the functions of tubulins.

Mechanical mapping of single membrane proteins at submolecular resolution

The capacity of proteins to carry out different functions is related to their ability to undergo conformation changes, which depends on the flexibility of protein structures. In this work, we applied a novel imaging mode based on indentation force spectroscopy to map quantitatively the flexibility of individual membrane proteins in their native, folded state at unprecedented submolecular resolution. Our results enabled us to correlate protein flexibility with crystal structure and showed that α-helices are stiff structures that may contribute importantly to the mechanical stability of membrane proteins, while interhelical loops appeared more flexible, allowing conformational changes related to function.

Effect of antimicrobial peptide-amide: indolicidin on biological membranes

Indolicidin, a cationic antimicrobial tridecapeptide amide, is rich in proline and tryptophan residues. Its biological activity is intensively studied, but the details how indolicidin interacts with membranes are not fully understood yet. We report here an in situ atomic force microscopic study describing the effect of indolicidin on an artificial supported planar bilayer membrane of dipalmitoyl phosphatidylcholine (DPPC) and on purple membrane of Halobacterium salinarum. Concentration dependent interaction of the peptide and membranes was found in case of DPPC resulting the destruction of the membrane. Purple membrane was much more resistant against indolicidin, probably due to its high protein content. Indolicidin preferred the border of membrane disks, where the lipids are more accessible. These data suggest that the atomic force microscope is a powerful tool in the study of indolicidin-membrane interaction.

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

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

DeStripe: frequency-based algorithm for removing stripe noises from AFM images

Background

Atomic force microscopy (AFM) is a relatively recently developed technique that shows a promising impact in the field of structural biology and biophysics. It has been used to image the molecular surface of membrane proteins at a lateral resolution of one nanometer or less. An immediate obstacle of characterizing surface features in AFM images is stripe noise. To better interpret structures at a sub-domain level, pre-processing of AFM images for removing stripe noises is necessary. Noise removal can be performed in either spatial or frequency domain. However, denoising processing in the frequency domain is a better solution for preserving edge sharpness.

Results

We have developed a denoising protocol, called DeStripe, for AFM bio-molecular images that are contaminated with heavy and fine stripes. This program adopts a divide-and-conquer approach by dividing the Fourier spectrum of the image into central and off-center regions for noisy pixels detection and intensity restoration; it is also applicable to other images interfered with high-density stripes such as those acquired by the scanning electron microscope. The denoising effect brought by DeStripe provides better visualization for image objects without introducing additional artifacts into the restored image.

Conclusions

The DeStripe denoising effect on AFM images is illustrated in the present work. It allows extracting extended information from the topographic measurements and implicitly enhances the molecular features in the image. All the presented images were processed by DeStripe with the raw image as the only input without any requirement for other prior information. A web service, http://biodev.cea.fr/destripe, is available for running DeStripe.

Introduction to atomic force microscopy

Atomic force microscopy (AFM) is an invaluable tool not only to obtain high-resolution topographical images, but also to determine certain physical properties of specimens, such as their mechanical properties and composition. In addition to the wide range of applications, from materials science to biology, this technique can be operated in a number of environments as long as the specimen is attached to a surface, including ambient air, ultra high vacuum (UHV), and most importantly for biology, in liquids. The versatility of this technique is also reflected by the wide range of sizes of the sample that can dealt with, such as atoms, molecules, molecular aggregates, and cells. Indeed, this technique enables biological problems to be tackled from the single-molecule point of view and it allows not only to see but also to touch the material under study (i.e., mechanical manipulation at the nanoscale), a fundamental source of information for its characterization. In particular, the study of the mechanical properties at the nanoscale of biomolecular aggregates constitute an important source of data to elaborate mechano-chemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.

Resonance energy transfer improves the biological function of bacteriorhodopsin within a hybrid material built from purple membranes and semiconductor quantum dots

Purple membrane (PM) from bacteria Halobacterium salinarum contains a photochromic protein bacteriorhodopsin (bR) arranged in a 2D hexagonal nanocrystalline lattice (Figure 1 ). Absorption of light by the protein-bound chromophore retinal results in pumping the protons through the PM creating an electrochemical gradient which is then used by the ATPases to energize the cellular processes. Energy conversion, photochromism, and photoelectrism are the inherent effects which are employed in many bR technical applications. bR, along with the other photosensitive proteins, is not able to deal with the excess energy of photons in UV and blue spectral region and utilizes less than 0.5% of the energy from the available incident solar light for its biological function. Here, we proceed with optimization of bR functions through the engineering of a "nanoconverter" of solar energy based on semiconductor quantum dots (QDs) tagged with the PM. These nanoconverters are able to harvest light from deep-UV to the visible region and to transfer this additionally collected energy to bR via Förster resonance energy transfer (FRET). We show that specific nanobio-optical and spatial coupling of QDs (donor) and bR retinal (acceptor) provide a means to achieve FRET with efficiency approaching 100%. We have finally demonstrated that the integration of QDs within PM significantly increases the efficiency of light-driven transmembrane proton pumping, which is the main bR biological function. This new QD-PM hybrid material will have numerous optoelectronic, photonic, and photovoltaic applications based on its energy conversion, photochromism, and photoelectrism properties.

AFM imaging and analysis of electrostatic double layer forces on single DNA molecules

Electrical double layer (EDL) forces develop between charged surfaces immersed in an electrolyte solution. Biological material surrounded by its physiological medium constitutes a case where these forces play a major role. Specifically, this work is focused on the study of the EDL force exerted by DNA molecules, a standard reference for the study of single biomolecules of nanometer size. The molecules deposited on plane substrates have been characterized by means of the atomic force microscope operated in the force spectroscopy imaging mode. Force spectroscopy imaging provides images of the topography of the DNA molecules, and of the EDL force spectrum. Due to the size of the molecule being much smaller than that of the tip, both the tip-substrate and tip-molecule interactions need to be considered in the analysis of the experimental results. We solve this problem by linearly superposing the two contributions. EDL force images are presented where DNA molecules are clearly resolved. The lateral resolution of the EDL force is discussed and compared with that of the topography. The method also allows the estimation of the DNA surface charge density, thereby obtaining reasonable values.

Applications of atomic force microscopy in biophysical chemistry of cells

This article addresses the question of what information and new insights atomic force microscopy (AFM) provides that are of importance and relevance to cellular biophysical chemistry research. Three enabling aspects of AFM are discussed: (a) visualization of membrane structural features with nanometer resolution, such as microvilli, ridges, porosomes, lamellapodia, and filopodia; (b) revealing structural evolution associated with cellular signaling pathways by time-dependent and high-resolution imaging of the cellular membrane in correlation with intracellular components from simultaneous optical microscopy; and (c) qualitative and quantitative measurements of single cell mechanics by acquisition of force-deformation profiles and extraction of Young's moduli for the membrane as well as cytoskeleton. A future prospective of AFM is also presented.

Visualization and structural analysis of the bacterial magnetic organelle magnetosome using atomic force microscopy

The unique ability of magnetotactic bacteria to navigate along a geomagnetic field is accomplished with the help of prokaryotic organelles, magnetosomes. The magnetosomes have well-ordered chain-like structures, comprising membrane-enveloped, nano-sized magnetic crystals, and various types of specifically associated proteins. In this study, we applied atomic force microscopy (AFM) to investigate the spatial configuration of isolated magnetosomes from Magnetospirillum magneticum AMB-1 in near-native buffer conditions. AFM observation revealed organic material with a approximately 7-nm thickness surrounding a magnetite crystal. Small globular proteins, identified as magnetosome-associated protein MamA, were distributed on the mica surface around the magnetosome. Immuno-labeling with AFM showed that MamA is located on the magnetosome surface. In vitro experiments showed that MamA proteins interact with each other and form a high molecular mass complex. These findings suggest that magnetosomes are covered with MamA oligomers in near-native environments. Furthermore, nanodissection revealed that magnetosomes are built with heterogeneous structures that comprise the organic layer. This study provides important clues to the supramolecular architecture of the bacterial organelle, the magnetosome, and insight into the function of the proteins localized in the organelle.

Curvature of purple membranes comprising permanently wedge-shaped bacteriorhodopsin molecules is regulated by lipid content

Purple membrane (PM) from Halobacterium salinarum has been studied by many groups and is commonly described as a flat 2-D crystalline membrane microdomain which contains a hexagonal crystalline lattice of bacteriorhodopsin (BR) trimers in a stoichiometric ratio of 10:1 between lipids and BR. BR is the key protein in the halobacterial photosynthetic system and acts as a light-driven proton pump. Upon absorption of a photon, BR undergoes a cyclic series of intramolecular changes, among them a transient "wedge-like" geometrical change of the protein due to a tilt in helix F, one of the seven alpha-helical domains of BR. Due to the strong coupling between the BRs in the crystalline lattice, this may affect membrane topography. In nature, only low light levels occur and the total number of BRs in the "wedge-shaped" state is negligible. For mutated PMs like PM-D85T and PM-D85N (PM-D85X, X = neutral residue), the change of the membrane topography can be triggered in a pH-dependent manner. PMs containing BR-D85X look like "cups" at certain pH values. How does nature deal with a mutated PM like PM-D96G/F171C/F219L (PM-Tri) which comprises permanently "wedge-shaped" BRs and how does this influence membrane assembly? Astonishingly, we observed that PM-Tri is flat. Obviously, the morphology of Halobacterium salinarum is highly conserved and requires flat PMs to be assembled. We found that the lipid content of PM-Tri is specifically altered to assemble a hexagonal crystalline PM-Tri lattice of flat topography.

Automated setpoint adjustment for biological contact mode atomic force microscopy imaging

Contact mode atomic force microscopy (AFM) is the most frequently used AFM imaging mode in biology. It is about 5-10 times faster than oscillating mode imaging (in conventional AFM setups), and provides topographs of biological samples with sub-molecular resolution and at a high signal-to-noise ratio. Unfortunately, contact mode imaging is sensitive to the applied force and intrinsic force drift: inappropriate force applied by the AFM tip damages the soft biological samples. We present a methodology that automatically searches for and maintains high resolution imaging forces. We found that the vertical and lateral vibrations of the probe during scanning are valuable signals for the characterization of the actual applied force by the tip. This allows automated adjustment and correction of the setpoint force during an experiment. A system that permanently performs this methodology steered the AFM towards high resolution imaging forces and imaged purple membrane at molecular resolution and live cells at high signal-to-noise ratio for hours without an operator.

Contact-mode high-resolution high-speed atomic force microscopy movies of the purple membrane

High-speed atomic force microscopy (HS-AFM) is becoming a reference tool for the study of dynamic biological processes. The spatial and time resolutions of HS-AFM are on the order of nanometers and milliseconds, respectively, and allow structural and functional characterization of biological processes at the single-molecule level. In this work we present contact-mode HS-AFM movies of purple membranes containing two-dimensional arrays of bacteriorhodopsin (bR). In high-resolution movies acquired at a 100 ms frame acquisition time, the substructure on individual bR trimers was visualized. In regions in between different bR arrays, dynamic topographies were observed and interpreted as motion of the bR trimers. Similarly, motion of bR monomers in the vicinity of lattice defects in the purple membrane was observed. Our findings indicate that the bR arrays are in a mobile association-dissociation equilibrium. HS-AFM on membranes provides novel perspectives for analyzing the membrane diffusion processes of nonlabeled molecules.

Tumor suppressor protein SMAR1 modulates the roughness of cell surface: combined AFM and SEM study

Background

Imaging tools such as scanning electron microscope (SEM) and atomic force microscope (AFM) can be used to produce high-resolution topographic images of biomedical specimens and hence are well suited for imaging alterations in cell morphology. We have studied the correlation of SMAR1 expression with cell surface smoothness in cell lines as well as in different grades of human breast cancer and mouse tumor sections.

Methods

We validated knockdown and overexpression of SMAR1 using RT-PCR as well as Western blotting in human embryonic kidney (HEK) 293, human breast cancer (MCF-7) and mouse melanoma (B16F1) cell lines. The samples were then processed for cell surface roughness studies using atomic force microscopy (AFM) and scanning electron microscopy (SEM). The same samples were used for microarray analysis as well. Tumors sections from control and SMAR1 treated mice as well as tissues sections from different grades of human breast cancer on poly L-lysine coated slides were used for AFM and SEM studies.

Results

Tumor sections from mice injected with melanoma cells showed pronounced surface roughness. In contrast, tumor sections obtained from nude mice that were first injected with melanoma cells followed by repeated injections of SMAR1-P44 peptide, exhibited relatively smoother surface profile. Interestingly, human breast cancer tissue sections that showed reduced SMAR1 expression exhibited increased surface roughness compared to the adjacent normal breast tissue. Our AFM data establishes that treatment of cells with SMAR1-P44 results into increase in cytoskeletal volume that is supported by comparative gene expression data showing an increase in the expression of specific cytoskeletal proteins compared to the control cells. Altogether, these findings indicate that tumor suppressor function of SMAR1 might be exhibited through smoothening of cell surface by regulating expression of cell surface proteins.

Conclusion

Tumor suppressor protein SMAR1 might be used as a phenotypic differentiation marker between cancerous and non-cancerous cells.

Structural information, resolution, and noise in high-resolution atomic force microscopy topographs

AFM has developed into a powerful tool in structural biology, providing topographs of proteins under close-to-native conditions and featuring an outstanding signal/noise ratio. However, the imaging mechanism exhibits particularities: fast and slow scan axis represent two independent image acquisition axes. Additionally, unknown tip geometry and tip-sample interaction render the contrast transfer function nondefinable. Hence, the interpretation of AFM topographs remained difficult. How can noise and distortions present in AFM images be quantified? How does the number of molecule topographs merged influence the structural information provided by averages? What is the resolution of topographs? Here, we find that in high-resolution AFM topographs, many molecule images are only slightly disturbed by noise, distortions, and tip-sample interactions. To identify these high-quality particles, we propose a selection criterion based on the internal symmetry of the imaged protein. We introduce a novel feature-based resolution analysis and show that AFM topographs of different proteins contain structural information beginning at different resolution thresholds: 10 A (AqpZ), 12 A (AQP0), 13 A (AQP2), and 20 A (light-harvesting-complex-2). Importantly, we highlight that the best single-molecule images are more accurate molecular representations than ensemble averages, because averaging downsizes the z-dimension and "blurs" structural details.

Voltage-induced morphological modifications in oocyte membranes containing exogenous K+ channels studied by electrochemical scanning force microscopy

We report on a novel use of electrochemical scanning force microscopy (SFM) for the investigation of morphological modifications occurring in plasma membranes containing voltage-gated ion channels, on membrane potential variation. Membrane patches of Xenopus laevis oocytes microinjected with exogenous KAT1 cRNA, deposited by a stripping method at the surface of a derivatized gold film in inside-out configuration, have been imaged by SFM in an electrochemical cell. A potentiostat was used to maintain a desired potential drop across the membrane. Performing imaging at potential values corresponding to open (-120 mV) and closed (+20 mV) states for KAT1, morphological differences in localized sample zones were observed. Particularly, cross-shaped features involving a significant membrane portion appear around putative channel locations. The reported approach constitutes the first demonstration of an SPM-based experimental technique suitable to investigate the rearrangements occurring to the plasma membrane containing voltage-gated channels on transmembrane potential variation.

Bioinspired nanoencapsulation of purple membranes

Embedding biological compounds, e.g. enzymes or whole cells, in solid host material seems to be a promising approach to widen their field of application far beyond the limits of natural conditions. In fields such as medicine and biotechnology, there is great interest in new methods to produce these types of composite materials in the form of micro- or nanosized particles. Such methods should be applicable to large amounts of substance. Inspired by one of nature's remarkable features-its ability to combine (bio)organic and inorganic components at the nanoscale-we developed a generic silica encapsulation method for biomolecules based on the concepts of polyelectrolyte layer adsorption followed by templated silica mineralization similar to biomineralization in diatoms. Application of this method to the model substance purple membrane (PM) resulted in a defined hybrid material with a nanoscale protective encapsulating silica shell providing a high barrier for the diffusion of low molecular weight molecules.

Past, present and future of atomic force microscopy in life sciences and medicine

To introduce this special issue of the Journal of Molecular Recognition dedicated to the applications of atomic force microscopy (AFM) in life sciences, this paper presents a short summary of the history of AFM in biology. Based on contributions from the first international conference of AFM in biological sciences and medicine (AFM BioMed Barcelona, 19-21 April 2007), we present and discuss recent progress made using AFM for studying cells and cellular interactions, probing single molecules, imaging biosurfaces at high resolution and investigating model membranes and their interactions. Future prospects in these different fields are also highlighted.

Vertebrate membrane proteins: structure, function, and insights from biophysical approaches

Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function.

Novel combination of atomic force microscopy and epifluorescence microscopy for visualization of leaching bacteria on pyrite

Bioleaching of metal sulfides is an interfacial process comprising the interactions of attached bacterial cells and bacterial extracellular polymeric substances with the surface of a mineral sulfide. Such processes and the associated biofilms can be investigated at high spatial resolution using atomic force microscopy (AFM). Therefore, we visualized biofilms of the meso-acidophilic leaching bacterium Acidithiobacillus ferrooxidans strain A2 on the metal sulfide pyrite with a newly developed combination of AFM with epifluorescence microscopy (EFM). This novel system allowed the imaging of the same sample location with both instruments. The pyrite sample, as fixed on a shuttle stage, was transferred between AFM and EFM devices. By staining the bacterial DNA with a specific fluorescence dye, bacterial cells were labeled and could easily be distinguished from other topographic features occurring in the AFM image. AFM scanning in liquid caused deformation and detachment of cells, but scanning in air had no effect on cell integrity. In summary, we successfully demonstrate that the new microscopic system was applicable for visualizing bioleaching samples. Moreover, the combination of AFM and EFM in general seems to be a powerful tool for investigations of biofilms on opaque materials and will help to advance our knowledge of biological interfacial processes. In principle, the shuttle stage can be transferred to additional instruments, and combinations of AFM and EFM with other surface-analyzing devices can be proposed.

Atomic force microscopy of recombinant adeno-associated virus-2 prepared by centrifugation

In order to decrease salt crystal formation, reduce the aggregation of viruses in atomic force microscopy (AFM) preparations and obtain an acceptable AFM image, the AFM sampling of viruses must be optimized. In this paper, centrifugal AFM sampling of recombinant adeno-associated virus-2 (rAAV-2) was used. The prepared rAAV-2 virus was imaged by AFM using the tapping mode in air. The results indicate that the rAAV-2 viruses prepared by centrifugal AFM sampling methods could be well imaged by AFM. The rAAV-2 viruses exhibited polymorphous particles in the AFM images. The preliminary off-line section analysis of the individual rAAV-2 virus particle indicated that the half-high widths of the large rAAV-2 particles ranged from 18 to 23 nm, while those of the small rAAV-2 particles ranged from 15 to 17 nm, which is almost in agreement with the results obtained by the off-line particle analysis of the rAAV-2 virus particles. Above all, the aggregation of different-sized rAAV-2 particles was directly imaged by AFM, which verifies the previous speculation that the large number (> ~31 nm) distribution of the mean diameter of rAAV-2 virus particles was probably caused by aggregation of rAAV-2 particles.

An easy method to discover cell membrane antigen with atomic force microscopy

Atomic force microscopy (AFM) obtains a high resolution at nanometer. In the current study, we found that, before and after adding CD34, CD44 or CD29 antibodies, the AFM images of mouse adipose tissue derived mesenchymal stem cells (ADMSCs) had significant changes in both cell morphous (shape) and the average roughness of cell membrane. However, there was no significant difference in the cell shape and the average roughness of cell membrane, after adding CD45 or CD144 antibodies. Therefore, we could use the AFM to scan cell shape or to calculate the average roughness changes of cell membrane to analyze the existence of cell membrane antigen qualitatively.

Structural models of the supramolecular organization of AQP0 and connexons in junctional microdomains

Membrane proteins perform many essential cellular functions. Over the last years, substantial advances have been made in our understanding of the structure and function of isolated membrane proteins. However, like soluble proteins, many membrane proteins assemble into supramolecular complexes that perform specific functions in specialized membrane domains. Since supramolecular complexes of membrane proteins are difficult to study by conventional approaches, little is known about their composition, organization and assembly. The high signal-to-noise ratio of the images that can be obtained with an atomic force microscope (AFM) makes this instrument a powerful tool to image membrane protein complexes within native membranes. Recently, we have reported high-resolution topographs of junctional microdomains in native eye lens membranes containing two-dimensional (2D) arrays of aquaporin-0 (AQP0) surrounded by connexons. While both proteins are involved in cell adhesion, AQP0 is a specific water channel whereas connexons form cell-cell communication channels with broad substrate specificity. Here, we have performed a detailed analysis of the supramolecular organization of AQP0 tetramers and connexon hexamers in junctional microdomains in the native lens membrane. We present first structural models of these junctional microdomains, which we generated by docking atomic models of AQP0 and connexons into the AFM topographs. The AQP0 2D arrays in the native membrane show the same molecular packing of tetramers seen in highly ordered double-layered 2D crystals obtained through reconstitution of purified AQP0. In contrast, the connexons that surround the AQP0 arrays are only loosely packed. Based on our AFM observations, we propose a mechanism that may explain the supramolecular organization of AQP0 and connexons in junctional domains in native lens membranes.

Nanomicrobiology

Recent advances in atomic force microscopy (AFM) are revolutionizing our views of microbial surfaces. While AFM imaging is very useful for visualizing the surface of hydrated cells and membranes on the nanoscale, force spectroscopy enables researchers to locally probe biomolecular forces and physical properties. These unique capabilities allow us to address a number of questions that were inaccessible before, such as how does the surface architecture of microbes change as they grow or interact with drugs, and what are the molecular forces driving their interaction with antibiotics and host cells? Here, we provide a flavor of recent achievements brought by AFM imaging and single molecule force spectroscopy in microbiology.

Intermediate filaments: from cell architecture to nanomechanics

Intermediate filaments (IFs) constitute a major structural element of animal cells. They build two distinct systems, one in the nucleus and one in the cytoplasm. In both cases, their major function is assumed to be that of a mechanical stress absorber and an integrating device for the entire cytoskeleton. In line with this, recent disease mutations in human IF proteins indicate that the nanomechanical properties of cell-type-specific IFs are central to the pathogenesis of diseases as diverse as muscular dystrophy and premature ageing. However, the analysis of these various diseases suggests that IFs also have an important role in cell-type-specific physiological functions.

Different interactions between the two sides of purple membrane with atomic force microscope tip

Atomic force microscopy (AFM) is known to be capable of measuring local surface charge density based on the DLVO model. However, it has failed to distinguish charge density difference between the extracellular and cytoplasmic sides of purple membrane (PM) in previous studies. In this paper, tapping-mode AFM with thioglycolate-modified tips was used to image PM in buffers of different salt concentrations. When imaged in 25 mM KCl buffer, the topography of membranes appeared to be of two different types, one flat and the other domelike. Such a difference was not observed in buffers of high salt concentrations. This suggests that the topography variation results from differences in electrostatic interaction between the AFM tip and the different membrane surfaces. With images of papain-digested PM and high-resolution images of membrane surface structure, we proved that the membrane surfaces with flat topography were on the extracellular side while the surfaces with domelike topography were on the cytoplasmic side. Hence, this provides a straightforward method to distinguish the two sides of PM without the requirement of high-resolution imaging. Force-distance curves clearly demonstrated the different tip-sample interactions. The force curves recorded on the extracellular side of PM were consistent with the DLVO model, so its surface charge density can be estimated well. However, the curves recorded on the cytoplasmic side had a much longer decay length, which is supposed to be relevant to the flexibility of the C-terminus of bacteriorhodopsin (bR).

Single Biomolecule Imaging with Frequency and Force Modulation in Tapping-Mode Atomic Force Microscopy

A new intermittent-contact atomic force microscopy (AFM) mode (frequency and force modulation AFM, FFM-AFM) has been recently proposed to characterize soft samples. This method uses excitation force frequency and amplitude modulation to eliminate bistability and reduce the tip-sample forces. This letter describes theoretical modeling of FFM-AFM applied to a single bacteriorhodopsin molecule on a substrate, showing that its cross section can be measured without damage, in contrast to conventional tapping-mode AFM. Speculations are made regarding nonideal conditions and the ability of FFM-AFM to perform quantitative nanoelasticity measurements.

Is the vascular endothelium under the control of aldosterone? Facts and hypothesis

Fluid and electrolyte balance in the human organism is controlled by aldosterone, a mineralocorticoid hormone of the suprarenal glands. The major target cells are localized in the kidney where the hormone controls transepithelial salt transport. Over the past few years, evidence has been accumulated that cells of the cardiovascular system are also targeted by the hormone. As an example, endothelial cells resemble similar mechanisms triggered by aldosterone as shown for the kidney. Although the pathological alterations induced by aldosterone excess are obvious, the physiological changes are largely unknown. On the basis of recent experiments, using atomic force microscopy as an imaging tool and a mechanical sensor, I present a hypothesis on the physiological role of aldosterone in endothelial function and its potential implications in the control of blood pressure.

Atomic force microscopy applied to study macromolecular content of embedded biological material

We demonstrate that atomic force microscopy represents a powerful tool for the estimation of structural preservation of biological samples embedded in epoxy resin, in terms of their macromolecular distribution and architecture. The comparison of atomic force microscopy (AFM) and transmission electron microscopy (TEM) images of a biosample (Caenorhabditis elegans) prepared following to different types of freeze-substitution protocols (conventional OsO4 fixation, epoxy fixation) led to the conclusion that high TEM stainability of the sample results from a low macromolecular density of the cellular matrix. We propose a novel procedure aimed to obtain AFM and TEM images of the same particular organelle, which strongly facilitates AFM image interpretation and reveals new ultrastructural aspects (mainly protein arrangement) of a biosample in addition to TEM data.

Emerging technologies for the molecular study of infertility, and potential clinical applications

The techniques currently used to treat infertility cases are quite limited in their capabilities, due to an incomplete understanding of the molecular activities of germ cells. Fortunately, several technologies are presently being researched that should aid the understanding of the various molecular causes of germ cell pathologies. This review discusses microarray technology, proteomics, metabolic profiling, the PolScope, atomic force microscopy and microfluidics. These technologies have all seen success in preliminary studies, and promise directly or indirectly to improve the low success rates of IVF and other related therapies. However, their widespread use in laboratories and clinics may not be seen until preliminary studies confirming their safety and effectiveness are published, and until standardized protocols for their utilization are established.

Using microcantilever deflection to detect HIV-1 envelope glycoprotein gp120

Microcantilevers have been used over the last decade to detect biomolecules from solution. Specific binding events on one surface of the microcantilever create a differential stress, resulting in measurable deflection. Here we use this principle to detect human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) gp120 from solution. We observed deflections approximately twice that of the baseline (in PBS) upon specific binding of gp120 to cantilevers decorated on one side with monoclonal antibodies (mAbs) A32 or T8. Subsequent incubation with mAb 17b (known to bind an A32-induced epitope on gp120) further increased deflection of A32- but not T8-presenting cantilevers. This work shows the capability of microcantilever deflection sensors to detect an induced-fit interaction at test concentrations of 8 microg/mL gp120 and 0.17 mg/mL 17b. Further development of this technique could lead to a portable, low-cost device for the effective detection of HIV-1.

Nanoscale exploration of microbial surfaces using the atomic force microscope

Atomic force microscopy (AFM) has recently opened a variety of novel possibilities for imaging and manipulating microbial surfaces in their native environment. While AFM imaging offers a means to visualize surface structures at high resolution and in physiological conditions, AFM force spectroscopy enables researchers to probe a variety of properties, including the unfolding pathways of single-membrane proteins, the elasticity of cell walls and surface macromolecules, and the molecular forces responsible for cell–cell and cell–solid interactions. These nanoscale analyses enable us to answer a number of questions that were difficult to address previously, such as: how does the surface architecture of microbes change as they grow or interact with antibiotics; what is the force required to unfold and extract a single membrane protein; and what are the molecular forces driving the interaction between a pathogen and a host or biomaterial surface? This review will expand on these issues.

Spatial resolution, information limit, and contrast transfer in piezoresponse force microscopy

Scanning probe-based ferroelectric domain imaging and patterning has attracted broad attention for use in the characterization of ferroelectric materials, ultrahigh density data storage, and nanofabrication. The viability of these applications is limited by the minimal domain size that can be fabricated and reliably detected by scanning probe microscopy. Here, the contrast transfer mechanism in piezoresponse force microscopy (PFM) of ferroelectric materials is analysed in detail. A consistent definition of resolution is developed both for the writing and the imaging processes, and the concept of an information limit in PFM is established. Experimental determination of the object transfer function and the subsequent reconstruction of an 'ideal image' is demonstrated. This contrast transfer theory provides a quantitative basis for image interpretation and allows for the comparison of different instruments in PFM. It is shown that experimentally observed domain sizes can be limited by the resolution of the scanning probe microscope to the order of tens of nanometres even though smaller domains, of the order of several nanometres, can be created.

Route of glucocorticoid-induced macromolecules across the nuclear envelope as viewed by atomic force microscopy

Glucocorticoids are vital steroid hormones. The physiologic activities of these hydrophobic molecules predominantly require translocation of glucocorticoid-initiated macromolecules (GIMs), proteins and mRNA transcripts, in and out of the nucleus, respectively. The bidirectional transport of GIMs is mediated by nuclear pore complexes (NPCs) that span the nuclear envelope at regular distances. The transport proceeds through the NPC central channel, whose interior is lined up by hydrophobic proteins. The NPC channel is assumed to dilate while hydrophobic cargos are being translocated through. Upon glucocorticoid injection into a glucocorticoid-sensitive cell, Xenopus laevis oocyte, and using atomic force microscopy, we have recently unraveled the long unexplored paths that GIMs take through the nuclear envelope and described interactions of GIMs with NPCs. In so doing, surprising and intriguing observations were made and the following conclusions were drawn: glucocorticoid-initiated proteins evoke NPC channel dilation before physical interaction with the NPC. NPC channel dilation is apparently transmitted through binding of glucocorticoid-induced proteins to NPC-associated filaments or yet unknown structures in the cytoplasmic nuclear envelope surface. The transport of both proteins and ribonucleoproteins seems to be non-randomly confined to local areas on either nuclear envelope site, the so-called hot spots.