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At least 163 records · Page 9Linked to original sources

Cadherin interaction probed by atomic force microscopy.

Single molecule atomic force microscopy was used to characterize structure, binding strength (unbinding force), and binding kinetics of a classical cadherin, vascular endothelial (VE)-cadherin, secreted by transfected Chinese hamster ovary cells as cis-dimerized full-length external domain fused to Fc-portion of human IgG. In physiological buffer, the external domain of VE-cadherin dimers is a approximately 20-nm-long rod-shaped molecule that collapses and dissociates into monomers (V-shaped structures) in the absence of Ca(2+). Trans-interaction of dimers is a low-affinity reaction (K(D) = 10(-3)-10(-5) M, k(off) = 1.8 s(-1), k(on) = 10(3)-10(5) M(-1) x s(-1)) with relatively low unbinding force (35-55 pN at retrace velocities of 200-4,000 nm x s(-1)). Higher order unbinding forces, that increase with interaction time, indicate association of cadherins into complexes with cumulative binding strength. These observations favor a model by which the inherently weak unit binding strength and affinity of cadherin trans-interaction requires clustering and cytoskeletal immobilization for amplification. Binding is regulated by low-affinity Ca(2+) binding sites (K(D) = 1.15 mM) with high cooperativity (Hill coefficient of 5.04). Local changes of free extracellular Ca(2+) in the narrow intercellular space may be of physiological importance to facilitate rapid remodeling of intercellular adhesion and communication.

Animals↗

Energy dissipation in atomic force microscopy and atomic loss processes.

Atomic scale dissipation is of great interest in nanomechanics and atomic manipulation. We present dissipation measurements with a linearized, ultra-small amplitude atomic force microscope which is capable of measuring dissipation at chosen, fixed separations. We show that the dynamic dissipation in the noncontact regime is of the order of a few 10-100 meV per cycle. This dissipation is likely due to the motion of a bistable atomic defect in the tip-surface region. In the contact regime we observe dc hysteresis associated with nanoscale plasticity. We find the hysteretic energy loss to be 1 order of magnitude higher for a silicon surface than for copper.

Journal Article↗

Atomic force microscopy and drug discovery.

Atomic force microscopy is being used ever more widely in biological imaging, because of its unique ability to provide structural information at the single molecule level and under near-physiological conditions. Detailed topographic images of potential drug targets, such as proteins and DNA, have been produced, and the folding of modular proteins has been studied using single-molecule force spectroscopy. Recently, atomic force microscopy has been used to examine ligand-protein and ligand-DNA interactions, and to begin to determine the architecture of multi-subunit proteins, including a member of the superfamily of ionotropic receptors. Atomic force microscopy is fast becoming a valuable addition to the pharmaceutical industry's toolkit.

DNA↗

Differentiating inclusion complexes from host molecules by tapping-mode atomic force microscopy.

Tapping-mode atomic force microscopy imaging under different cantilever vibration amplitudes has been used to differentiate the host beta-cyclodextrin nanotubes from retinal/beta-cyclodextrin inclusion complex nanotubes. It was observed that both compounds were deformed differently by the applied probe force because of their different local rigidity. This change in the elasticity properties can be explained as a consequence of the inclusion process. This method shows that tapping-mode atomic force microscopy is an useful tool to map soft sample elasticity properties and to distinguish inclusion complexes from their host molecules on the basis of their different mechanical response.

Biophysical Phenomena↗

The structure of intramolecular triplex DNA: atomic force microscopy study.

We applied atomic force microscopy (AFM) for direct imaging of intramolecular triplexes (H-DNA) formed by mirror-repeated purine-pyrimidine repeats and stabilized by negative DNA supercoiling. H-DNA appears in atomic force microscopy images as a clear protrusion with a different thickness than DNA duplex. Consistent with the existing models, H-DNA formation results in a kink in the double helix path. The kink forms an acute angle so that the flanking DNA regions are brought in close proximity. The mobility of flanking DNA arms is limited compared with that for cruciforms and three-way junctions. Structural properties of H-DNA may be important for promoter-enhancer interactions and other DNA transactions.

Base Sequence↗

Recent progress in the application of atomic force microscopy imaging and force spectroscopy to microbiology.

Atomic force microscopy imaging and force spectroscopy have recently opened a range of novel applications in microbiology. During the past two years, rapid advances have been made using atomic force microscopy to visualize the surface structure of two-dimensional bacterial protein crystals, biofilms and individual cells in physiological conditions. There has also been remarkable progress in using force spectroscopy to measure biomolecular interactions and physical properties of microbial surfaces. Specific highlights include the imaging and manipulation of membrane proteins at the subnanometer level, the observation of the surface of living cells at high resolution, the mapping of local properties such as surface charges, the measurement of elastic properties of cell-surface constituents and the probing of cellular interactions using functionalized probes.

Bacteria↗

Scratching the sporocyst surface: characterisation of European Aggregata species by atomic force microscopy.

The application of atomic force microscopy to the understanding of surface structure and atomic-scale measurements on the sporocyst of European Aggregata species, intracellular coccidia of the cephalopods Octopus vulgaris and Sepia officinalis, is presented here. Using the roughness mean surface (RMS) as an index, we reveal texture to be a key parameter for characterisation of the sporocyst surface properties, which resolve the historical synonymy within the European Aggregatidae. Roughness measurements from RMS algorithms may also be an important diagnostic taxonomic character for the differentiation of Aggregata species in the future.

Algorithms↗

Scanning electron microscopy studies of protein-functionalized atomic force microscopy cantilever tips.

Protein-functionalized atomic force microscopy (AFM) tips have been used to investigate the interaction of individual ligand-receptor complexes. Herein we present results from scanning electron microscopy (SEM) studies of protein-functionalized AFM cantilever tips. The goals of this study were (1) to examine the surface morphology of protein-coated AFM tips and (2) to determine the stability of the coated tips. Based on SEM images, we found that bovine serum albumin (BSA) in solution spontaneously adsorbed onto the surface of silicon nitride cantilevers, forming a uniform protein layer over the surface. Additional protein layers deposited over the initial BSA-coated surface did not significantly alter the surface morphology. However, we found that avidin-functionalized tips were contaminated with debris after a series of force measurements with biotinylated agarose beads. The bound debris presumably originated from the transfer of material from the agarose bead. This observation is consistent with the observed deterioration of functional activity as measured in ligand-receptor binding force experiments.

Adsorption↗

Atomic force microscopy of plant chromosomes.

Atomic force microscopy has been used to image plant chromosomes from standard preparations without staining or coating. This has enabled the collection of high-resolution three-dimensional data on surface structure. The technique has been further applied to the imaging of C-banded chromosomes revealing structural changes resulting from the banding treatment. The bands were observed as localized areas of high relief.

Chromosome Banding↗

[Study of microorganism genome DNA by atomic force microscopy].

The potential of atomic force microscopy (AFM) for the investigation of peculiarities of microorganisms genome structure is demonstrated. AFM images of phage lambda DNA linear molecules and supercoiled mica in buffer solution was imaged in air. New experimental method of DNA stretching based on using amino-modified mica with a decreased surface density of active amino-groups is proposed. Stretched molecules of phage lambda DNA were imaged by AFM.

Bacteriophage lambda↗

Glassy cholesteric structure: thickness variation induced by electron radiation in transmission electron microscopy investigated by atomic force microscopy.

During the observation of glassy cholesteric liquid crystals in transmission electron microscopy (TEM), a new contrast is created or enhanced by electron radiation which has a direct relationship with the periodic microstructure of the specimen. In this paper, we investigate the variations of the sample thickness and mass density as possible causes of this irradiation contrast. By means of observations in atomic force microscopy (AFM) coupled to TEM, we compared the surface corrugations of non-irradiated and irradiated specimens. It is shown that the final contrast is the result of several processes. including fracture during ultramicrotomy and mass loss during irradiation. Mass loss acts as an etching, and hence results in a decrease of the sample thickness. The etching depends on the initial molecular orientation, thus evidencing the latent structure. An electron channelling mechanism is suggested to explain this behaviour.

Journal Article↗

Single protein misfolding events captured by atomic force microscopy.

Using single protein atomic force microscopy (AFM) techniques we demonstrate that after repeated mechanical extension/relaxation cycles, tandem modular proteins can misfold into a structure formed by two neighboring modules. The misfolding is fully reversible and alters the mechanical topology of the modules while it is about as stable as the original fold. Our results show that modular proteins can assume a novel misfolded state and demonstrate that AFM is able to capture, in real time, rare misfolding events at the level of a single protein.

Connectin↗

Feeling the forces: atomic force microscopy in cell biology.

Atomic force microscopy allows three-dimensional imaging and measurements of unstained and uncoated biological samples in air or fluid. Using this technology it offers resolution on the nanometer scale and detection of temporal changes in the mechanical properties, i.e. surface stiffness or elasticity in live cells and membranes. Various biological processes including ligand-receptor interactions, reorganization, and restructuring of the cytoskeleton associated with cell motility that are governed by intermolecular forces and their mode of detection will be discussed.

Animals↗

The heptameric prepore of a staphylococcal alpha-hemolysin mutant in lipid bilayers imaged by atomic force microscopy.

We have used atomic force microscopy to study the oligomeric state of a genetically engineered mutant of staphylococcal alpha-hemolysin (alphaHL-H5) that can be arrested as a "prepore" assembly intermediate. AFM images of alphaHL-H5 on supported bilayers of a fluid-phase lipid, egg-yolk phosphatidylcholine (egg-PC), under conditions that lock alphaHL-H5 into the prepore state, clearly show a heptameric structure for many individual oligomers. The central dent of the prepore has a diameter of 3.2 +/- 0.2 nm. The distance between the centers of mass of neighboring subunits is 2.8 +/- 0.3 nm. The heptamer has an average diameter of 8.9 +/- 0.6 nm. These results support a recently proposed pathway for the assembly of alpha-hemolysin.

Bacterial Toxins↗

Investigating the nature of branching in pectin by atomic force microscopy and carbohydrate analysis.

Atomic force microscopy (AFM) has been used to investigate the nature of the long branches attached to pectin which were described in a previous report [Round, A. N.; MacDougall, A. J.; Ring, S. G.; Morris, V. J. Carbohydr. Res. 1997, 303, 251-253]. Analysis of the AFM images and comparison with neutral sugar and linkage analyses of the two pectin fractions suggest that the distribution and total amount of branches observed do not correspond with the pattern of neutral sugar distribution. It is thus postulated that the long chains consist of polygalacturonic acid, attached via an as yet undetermined linkage to the pectin backbone, with the neutral sugars present as short, undetected branches. This explanation would have important implications for the nature of 'in situ' pectin networks within plant cell walls and models of gelation in commercial extracted pectin, and the existence of significant branching will markedly influence the viscosity of extracted pectins.

Carbohydrates↗