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PubMed2001

Microstructure of aggregated and nonaggregated kappa-carrageenan helices visualized by atomic force microscopy.

Gelation of kappa-carrageenan is believed to involve two steps: helix formation on cooling and a further specific cation (salt) induced side-by-side aggregation of helices. Samples that should contain aggregated and also nonaggregated "helices" of kappa-carrageenan were prepared in aqueous solutions, spread onto freshly cleaved mica surfaces, and visualized under butanol using atomic force microscopy. In the presence of an excessive amount of a gel-promoting salt, KCl, kappa-carrageenan appeared to form rigid rodlike structures considered as large aggregates of double helices. Even when the side-by-side interhelical aggregation was suppressed by diluting random coiled solutions prior to cooling, by adding an aggregation-impeding salt, NaI, or by transforming kappa-carrageenan into the tetramethylammonium (TMA) salt, branched rodlike structures were still evident, suggesting that the side-by-side aggregation of helices is not a prerequisite for kappa-carrageenan to form a network structure, at least locally. Even in the absence of factors that promote side-by-side aggregation, kappa-carrageenan helices appeared to be capable of associating and forming gel networks.

Carbohydrate Conformation↗

PubMed2004

Structure of small actin-containing liposomes probed by atomic force microscopy: effect of actin concentration & liposome size.

Actin-containing liposomes were prepared via extrusion through 400 and 600 nm pore diameter membranes at different monomeric actin concentrations in low ionic strength buffer (G-buffer). After subjecting the liposome dispersions to high ionic strength polymerization buffer (F-buffer), topological changes in liposome structure were studied using atomic force microscopy (AFM). Paired dumbbell, horseshoelike, and disklike assemblies were observed for actin-containing liposomes extruded through 400 and 600 nm pore diameter membranes. The topology of actin-containing liposomes was found to be highly dependent on both liposome size and actin concentration. At 1 mg/mL actin, the actin-containing liposomes transformed into a disklike shape, whereas, at 5 mg/mL actin, the actin-containing liposomes retained a spherical shape. On the basis of these observations, we hypothesize that actin could either polymerize on the surface of the inner leaflet of the liposome membrane or polymerize in the aqueous core of the liposome. We explain the associated shape changes induced in actin-containing liposomes on the basis of the hypothesized mechanism of actin polymerization inside the liposomes. At higher actin concentrations (5 mg/mL), we observed membrane-induced actin self-assembly in G-buffer, which implies that G-actin is able to interact directly with lipid bilayers at sufficiently high concentrations.

Actins↗

PubMed2004

Atomic force microscopy assisted immobilization of lipid vesicles.

We report on a new approach to direct the immobilization of unilamellar lipid vesicles on substrate-supported lipid bilayers in a spatially confined manner. The adsorption of vesicles from solution is limited to areas of disorder in the bilayers, which is induced by scanning a pattern in situ with an atomic force microscopy (AFM) tip using high imaging forces. Lines of vesicles with a length exceeding 25 microm and a width corresponding to that of a single surface-immobilized vesicle have been fabricated. The adsorbed vesicles are effectively immobilized and do not desorb spontaneously. However, AFM with forces of several nanoNewtons allows one to displace vesicles selectively. The novel methodology described, which may serve as a platform for research on proteins incorporated in the lipid bilayers comprising the vesicles, does not require chemical labeling of the vesicles to guide their deposition.

Adsorption↗

PubMed2002

Contact mechanics modeling of pull-off measurements: effect of solvent, probe radius, and chemical binding probability on the detection of single-bond rupture forces by atomic force microscopy.

Pull-off forces for chemically modified atomic force microscopy tips in contact with flat substrates coated with receptor molecules are calculated using a Johnson, Kendall, and Roberts contact mechanics model. The expression for the work of adhesion is modified to account for the formation of discrete numbers of chemical bonds (nBonds) between the tip and substrate. The model predicts that the pull-off force scales as nBonds(1/2), which differs from a common assumption that the pull-off force scales linearly with nBonds. Periodic peak progressions are observed in histograms generated from hundreds of computed pull-off forces. The histogram periodicity is the signature of discrete chemical interactions between the tip and substrate and allows estimation of single-bond rupture forces. The effects of solvent, probe tip radius, and chemical binding probability on the detection of single-bond forces are examined systematically. A dimensionless parameter, the effective force resolution, is introduced that serves as a quantitative predictor for determining when periodicity in force histograms can occur. The output of model is compared to recent experimental results involving tips and substrates modified with self-assembled monolayers. An advantage of this contact mechanics approach is that it allows straightforward estimation of solvent effects on pull-off forces.

Journal Article↗

PubMed2001

Imaging of single hairpin ribozymes in solution by atomic force microscopy.

The hairpin ribozyme is a short endonucleolytic RNA motif isolated from a family of related plant virus satellite RNAs. It consists of two independently folding domains, each comprising two Watson-Crick helices flanking a conserved internal loop. The domains need to physically interact (dock) for catalysis of site-specific cleavage and ligation reactions. Using tapping-mode atomic force microscopy in aqueous buffer solution, we were able to produce high quality images of individual hairpin ribozyme molecules with extended terminal helices. Three RNA constructs with either the essential cleavage site guanosine or a detrimental adenosine substitution and with or without a 6-nt insertion to confer flexibility to the interdomain hinge show structural differences that correlate with their ability to form the active docked conformation. The observed contour lengths and shapes are consistent with previous bulk-solution measurements of the transient electric dichroism decays for the same RNA constructs. The active docked construct appears as an asymmetrically docked conformation that might be an indication of a more complicated docking event than a simple collapse around the interdomain hinge.

Base Sequence↗

PubMed2000

Atomic force microscopy reveals the mechanical design of a modular protein.

Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering.

Biomechanical Phenomena↗

PubMed1999

Voltage and pH-induced channel closure of porin OmpF visualized by atomic force microscopy.

Gram-negative bacteria are protected by an outer membrane in which trimeric channels, the porins, facilitate the passage of small solutes. The pores are formed by membrane-spanning antiparallel beta-strands, which are connected by short turns on the periplasmic side and long loops on the extracellular side. Voltage and pH-dependent conformational changes of these extracellular loops have now been visualized by atomic force microscopy of two-dimensional crystals of Escherichia coli porin OmpF. The observed conformational changes accompany the closure of the channel entrance, and suggest that this is a mechanism that the cells have evolved to protect themselves from drastic changes of the environment.

Bacterial Proteins↗

PubMed2005

Stoichiometry-dependent formation of quantum dot-antibody bioconjugates: a complementary atomic force microscopy and agarose gel electrophoresis study.

The unique advantages of quantum dot (QD) bioconjugates have motivated their application in biological assays. However, physical characterization of bioconjugated QDs after surface modification has often been overlooked. Here, biotinylated antibodies (biotin-IgG) were attached to commercial streptavidin-conjugated quantum dots (strep-QDs) at different stoichiometric ratios, and these QD bioconjugates were characterized with atomic force microscopy and discontinuous sodium dodecyl sulfate agarose gel electrophoresis (SDS-AGE). The results from these complementary analytical techniques showed that the molar ratio determined the relative sizes, molecular weights and morphologies of the QD bioconjugates. Additionally, the novel discontinuous SDS-AGE analysis confirmed specific binding between biotin-IgG and strep-QDs. Researchers who design QD bioconjugates for cell-based assays should consider stoichiometry-dependent differences in the physical properties of their QD bioconjugates.

Antibodies↗

PubMed2005

Analysis of interaction between DNA and Deinococcus radiodurans PprA protein by atomic force microscopy.

A DNA repair-promoting protein, PprA, was isolated from a radiation resistant bacterium, Deinococcus radiodurans [I. Narumi, K. Sato, S. Cui, T. Funayama, S. Kitayama, H. Watanabe, PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation, Mol. Microbiol. 54 (2004) 278-285]. Despite several studies, however, the function of PprA is not still clear. We used atomic force microscopy (AFM) to elucidate the role of this protein in the DNA repair pathway. In the present study, interaction between the linear DNA and PprA protein was imaged and analyzed by AFM without any fixation or staining. Though both end-bound and internally bound PprA was observed, the affinity of the end-bound protein was greater considering the proportion of features of binding analyzed by AFM. In some conditions, looping forms of the DNA-PprA complex were observed. Gel filtration high performance liquid chromatography (HPLC) was also conducted to estimate the molecular weight of this protein. The result of the HPLC analysis suggested that PprA formed multimers in buffer solution without DNA.

Bacterial Proteins↗

PubMed2006

The mechanical properties of E. coli type 1 pili measured by atomic force microscopy techniques.

The first step in the encounter between a host and a pathogen is attachment to the host epithelium. For uropathogenic Escherichia coli, these interactions are mediated by type 1 and P adhesive pili, which are long (approximately 1 microm) rods composed of more than 1000 protein subunits arranged in a helical structure. Here we used single-molecule atomic force microscopy to study the mechanical properties of type 1 pili. We found that type 1 pili readily extend under an applied force and that this extensibility is the result of unwinding the pilus rod's helical quaternary structure. The forced unraveling is also reversible, with helical rewinding taking place under considerable forces (approximately 60 pN). These data are similar to those obtained on P pili using optical tweezers, indicating that these are conserved properties of uropathogenic E. coli pili. We also show that our data can readily be reproduced using Monte Carlo simulation techniques based on a two-state kinetic model. This model provides a simple way to extrapolate the mechanical behavior of pili under a wide range of forces. We propose that type 1 pilus unraveling is an essential mechanism for absorbing physiological shear forces encountered during urinary tract infections and probably essential for adhesion and colonization of the bladder epithelium.

Biomechanical Phenomena↗

PubMed2001

Imaging the native structure of the chaperone protein GroEL without fixation using atomic force microscopy.

Most sample preparation methods for scanning probe or electron microscopy require that biomolecules, such as proteins, be fixed. Fixation destroys the molecular functionality and can possibly affect the true molecular structure. Here we report sample preparation conditions that allow the imaging of an unfixed protein, GroEL, under in-vivo conditions, by atomic force microscopy. Under these conditions, the protein should maintain its native structure and biological activity. The typical toroidal shape with pore of the GroEL complex was easily visible in the images. Images of a single complex show dimensions that agree well with crystallographic data. Under in-vivo conditions, it should be possible to study the biological activity and function of proteins.

Chaperonin 60↗

PubMed2006

Viscoelastic properties of zonal articular chondrocytes measured by atomic force microscopy.

OBJECTIVE: Articular chondrocytes respond to chemical and mechanical signals depending on their zone of origin with respect to distance from the tissue surface. However, little is known of the zonal variations in cellular mechanical properties in cartilage. The goal of this study was to determine the zonal variations in the elastic and viscoelastic properties of porcine chondrocytes using atomic force microscopy (AFM), and to validate this method against micropipette aspiration. METHODS: A theoretical solution for stress relaxation of a viscoelastic, incompressible, isotropic surface indented with a hard, spherical indenter (5 microm diameter) was derived and fit to experimental stress-relaxation data for AFM indentation of chondrocytes isolated from the superficial or middle/deep zones of cartilage. RESULTS: The instantaneous moduli of chondrocytes were 0.55+/-0.23 kPa for superficial cells (S) and 0.29+/-0.14 kPa for middle/deep cells (M/D) (P<0.0001), and the relaxed moduli were 0.31+/-0.15 kPa (S) and 0.17+/-0.09 kPa (M/D) (P<0.0001). The apparent viscosities were 1.15+/-0.66 kPas (S) and 0.61+/-0.69 kPa-s (M/D) (P<0.0001). Results from the micropipette aspiration test showed similar cell moduli but higher apparent viscosities, indicating that mechanical properties measured by these two techniques are similar. CONCLUSION: Our findings suggest that chondrocyte biomechanical properties differ significantly with the zone of origin, consistent with previous studies showing zonal differences in chondrocyte biosynthetic activity and gene expression. Given the versatility and dynamic testing capabilities of AFM, the ability to conduct stress-relaxation measurements using this technique may provide further insight into the viscoelastic properties of isolated cells.

Animals↗

PubMed2005

Localization of the lipopolysaccharide-binding protein in phospholipid membranes by atomic force microscopy.

Lipopolysaccharides (LPS; endotoxin) activate immunocompetent cells of the host via a transmembrane signaling process. In this study, we investigated the function of the LPS-binding protein (LBP) in this process. The cytoplasmic membrane of the cells was mimicked by lipid liposomes adsorbed on mica, and the lateral organization of LBP in these membranes and its interaction with LPS aggregates were characterized by atomic force microscopy. Using cantilever tips functionalized with anti-LBP antibodies, single LBP molecules were localized in the membrane at low concentrations. At higher concentrations, LBP formed clusters of several molecules and caused cross-linking of lipid bilayers. The addition of LPS to LBP-containing liposomes led to the formation of LPS domains in the membranes, which could be inhibited by anti-LBP antibodies. Thus, LBP mediates the fusion of lipid membranes and LPS aggregates.

Acute-Phase Proteins↗

PubMed2005

Liquid mechanical behavior of mixed monolayers of amino and alkyl silanes by atomic force microscopy.

The adsorption of mixed terminally aminated organosilyl compounds with long-chain n-alkyltrichlorosilanes on silica substrates has been studied by FTIR and AFM to deposit and study DNA. By optimization of deposition conditions, the mixed monolayers were found to be well organized and homogeneous. The amino group was protected to obtain a reproducible grafting and then deprotected after the film formation. In addition, atomic force microscopy (AFM) studies in both dynamical modes, amplitude modulation and frequency modulation, reveal that the layer behaves as a fluid as measured by the tip-cantilever and has a smaller characteristic time than the tip-cantilever. For three amplitudes, the experimental frequency shifts have been modeled for a fluidlike layer crossed by the tip. Finally, we show that this new fluidlike monolayer is suitable for DNA deposition and AFM studies.

Microscopy, Atomic Force↗

PubMed1997

Observation of metastable Abeta amyloid protofibrils by atomic force microscopy.

BACKGROUND: Brain amyloid plaque, a diagnostic feature of Alzheimer's disease (AD), contains an insoluble fibrillar core that is composed primarily of variants of the beta-amyloid protein (Abeta). As Abeta amyloid fibrils may initiate neurodegeneration, the inhibition of fibril formation is a possible therapeutic strategy. Very little is known about the early steps of the process, however. RESULTS: Atomic force microscopy was used to follow amyloid fibril formation in vitro by the Abeta variants Abeta1-40 and Abeta1-42. Both variants first form small ordered aggregates that grow slowly and then rapidly disappear, while prototypical amyloid fibrils of two discrete morphologies appear. Abeta1-42 aggregates much more rapidly than Abeta1-40, which is consistent with its connection to early-onset AD. We propose that the metastable intermediate species be called Abeta amyloid protofibrils. CONCLUSIONS: Abeta protofibrils are likely to be intermediates in the in vitro assembly of Abeta amyloid fibrils, but their in vivo role has yet to be determined. Numerous reports of a nonfibrillar form of Abeta aggregate in the brains of individuals who are predisposed to AD suggest the existence of a precursor form, possibly the protofibril. Thus, stabilization of Abeta protofibrils may be a useful therapeutic strategy.

Alzheimer Disease↗

PubMed2006

Atomic force microscopy visualization of poly(urethane urea) microphase rearrangements under aqueous environment.

Polyurethane biomaterials are a critically important class of polymers used in a variety of medical devices. It has been suggested that the good blood compatibility of polyurethanes arises from nanoscale chemical heterogeneities at the surface as a consequence of the microphase separated morphology. In this study, we used tapping mode atomic force microscopy with phase imaging under aqueous conditions to visualize the distribution of the surface microphases for a series of poly(urethane urea) block co-polymers with varying hard segment content. The surfaces were prehydrated for 24 h under a flow of 1 mM phosphate buffer. Topographic images showed the formation of nanometer-sized raised features on the surface, having lateral dimensions of 50-70 nm and heights of 10-15 nm. Phase images, reflecting the local distribution of the mechanical properties under aqueous conditions, were quite different from those obtained in ambient conditions, consistent with water-induced structural reorientation. Images suggest that there is little soft phase material at the polymer surface in the presence of water, while images acquired after dehydration of the samples show that the surface layer remains rich in hard domains, indicating that the films do not return to their original states over the time period studied.

Microscopy, Atomic Force↗

PubMed2005

Atomic force microscopy and photon correlation spectroscopy: two techniques for rapid characterization of liposomes.

The direct evaluation of the heterogeneity of the particle population of nanometric drug delivery systems as liposomes is difficult to achieve owing to the dimension and the carrier characteristics. The influence of the lipidic ratio and composition on the physical stability of liposomes during their storage was investigated using atomic force microscopy (AFM) and photon correlation spectroscopy (PCS). Liposomes were made by a mixture of different lipids and obtained using distinct methods of preparation. AFM images, acquired immediately after the deposition of the sample on mica surface, clearly showed the spherical shape of the lipidic vesicles. In all the 7 months of the experiment, the average sizes of the different liposomes evaluated using the two techniques were comparable. According to PCS analysis, AFM images confirmed that almost all the diversified vesicular systems tended to form aggregates during their storage; this loss of stability was strengthened by the increase of polydispersity index value. The different behaviours observed were to ascribe to the lipidic composition more than the methods of liposome preparation. In conclusion, AFM technique owing to the relative simplicity cold be useful for the technological control of size distribution profile according to the preparative factors and moreover to the batch-to-batch reproducibility.

Drug Carriers↗

PubMedDate not supplied

C-banding visualized by atomic force microscopy.

C-banding is a method used for studying chromosome rearrangements near centromeres and for investigating polymorphisms. In human chromosomes, the C-bands are located at the centromere of all the chromosomes and the distal long arm of the Y chromosome. In this study, we aimed to detect the structural changes in chromosomes during the stages of C-banding by atomic force microscopy. We observed crater-like structures in the chromosomes after 2xSSC (saline sodium citrate) treatment and measured the relative difference between the heights of chromatid and centromere of the chromosomes. Results showed that the relative difference was 3 nm in chromosomes 1, 9, 16, and Y, whereas in the other chromosomes this value was 11.6 nm. After Giemsa staining, the relative difference increased by a factor of 16 in chromosomes 1, 9, 16, and Y. The other chromosomes showed no such increase, which is in accordance with our suggestion that nonhiston proteins associated with DNA in constitutive heterochromatin can make the constitutive heterochromatin resistant to C-banding.

Azure Stains↗