Atomic force microscopy analysis of the Huntington protein nanofibril formation.
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Carrier Proteins↗
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Investigation of the felodipine glassy state by atomic force microscopy.
The glassy state of felodipine was prepared by melting crystals of felodipine on a clean glass slide and cooling to room temperature. It has been confirmed that glassy felodipine is a metastable state, and undergoes transformation to the more stable crystalline form. Crystallization occurred slowly and spontaneously at room temperature, below the glassy state transition temperature (Tg). The contact mode of atomic force microscopy was used for topographical imaging of the glassy and crystalline states of felodipine. When the glassy felodipine region next to the recrystallized zone was exposed to controlled mechanical stress through the tip, rapid additional crystallization was observed. This crystallization process can be induced and imaged in real time by atomic force microscopy.
Calcium Channel Blockers↗
Protein crystals as scanned probes for recognition atomic force microscopy.
Lysozyme crystal growth has been localized at the tip of a conventional silicon nitride cantilever through seeded nucleation. After cross-linking with glutaraldehyde, lysozyme protein crystal tips image gold nanoparticles and grating standards with a resolution comparable to that of conventional tips. Force spectra between the lysozyme crystal tips and surfaces covered with antilysozyme reveal an adhesion force that drops significantly upon blocking with free lysozyme, thus confirming that lysozyme crystal tips can detect molecular recognition interactions.
Biosensing Techniques↗
Structure of human chromosomes studied by atomic force microscopy. Part II. Relationship between structure and cytogenetic bands.
In the first part of this work, human chromosomes were characterized by atomic force microscopy (AFM) in air and in aqueous solution. The analysis of the images suggests that the last level of organization consists of a radial arrangement of chromatin loops which are anchored to a fiber which is folded giving a pattern of bands which differs in volume. Here the pattern of bands observed by AFM is compared to the cytogenetic map at the 850-band level. Thus thicker and thinner bands are identified as G and R bands, respectively. Finally a model is proposed which links genome sequence, cytogenetics, and chromosome structure.
Chromatids↗
Atomic force microscopy investigation of isolated virions of murine leukemia virus.
Virions of mouse leukemia virus spread on glass substrates were visualized by atomic force microscopy. The size distribution mode was 145 nm, significantly larger than that for human immunodeficiency virus particles. The distribution of particle sizes is broad, indicating that no two particles are likely identical in content or surface features. Virions possess knoblike protrusions, which may represent vestiges of budding from cell membranes. Particles which split open allowed imaging of intact cores with diameters of 65 nm. They also permitted estimation of viral shell thickness (35 to 40 nm) and showed the presence of a distinct trough between the shell and the core surface.
Animals↗
Atomic force microscopy of the proteasome.
The proteasome should be an ideal molecule for studies on large enzymatic complexes, given its multisubunit and modular structure, compartmentalized design, numerous activities, and its own means of regulation. Considering the recent increased interest in the ubiquitin-proteasome pathway, it is surprising that biophysical approaches to study this enzymatic assembly are applied with limited frequency. Methods including atomic force microscopy, fluorescence spectroscopy, surface plasmon resonance, and high-pressure procedures all have gained popularity in characterization of the proteasome. These methods provide significant and often unexpected insight regarding the structure and function of the enzyme. This chapter describes the use of atomic force microscopy for dynamic structural studies of the proteasome.
Animals↗
Water molecule clusters measured at water/air interfaces using atomic force microscopy.
During the tip approach to hydrophobic surfaces like the water/air interface, the measured interaction force reveals a strong attraction with a range of approximately 250 nm at some points along the interface. The range of this force is approximately 100 times larger than the measured for gold (approximately 3 nm) and 10 times larger than the one for hydrophobic silicon surfaces (approximately 25 nm). At other points the interface exerts a medium range repulsive force growing stepwise as the tip approaches the interface plane, consequently the hydrophobic force is a strong function of position. To explain these results we propose a model where the force on the tip is associated with the exchange of a small volume of the interface with a dielectric permittivity epsilon(int) by the tip with a dielectric permittivity epsilon(tip). By assuming a oscillatory spatial dependence for the dielectric permittivity it is possible to fit the measured force profiles. This dielectric spatial variation was associated with the orientation of the water molecules arrangement in the interfacial region. Small nanosized hydrogen-bond connected cages of water molecules present in bulk water at the interface are oriented by the interfacial electric field generated by the water molecules broken bonds, one broken hydrogen bond out of every four. This interfacial field orients small clusters formed by approximately 100 water molecules into larger clusters (approximately 100 nm). In the limit of small (less than 5 nm thick) water molecule cages we have modeled the static dielectric permittivity (epsilon) as the average response of those cages. In these regions the dielectric permittivity for water/air interfaces decreases monotonically from the bulk value epsilon approximately 80 to approximately 2 at the interface. For regions filled with medium size cages, the tip senses the structure of each cage and the static dielectric permittivity is matched to the geometrical features of these cages sized approximately 25 to 40 nm. Interfacial electric energy density values were calculated using the electric field intensity and the dielectric permittivity obtained by the fitting of the experimental points. The integration of the electric energy density along the interfacial region gives a value of 0.072 J m(-2) for interfacial energy density for points where the hydrophobic force has a range of approximately 250 nm. Regions formed by various clusters result in lower values of the interfacial energy density.
Gold↗
Atomic-force-microscopy imaging and molecular-recognition-force microscopy of recrystallized heterotetramers comprising an S-layer-streptavidin fusion protein.
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Crystallization↗
Structural analysis using atomic force microscopy of the surface of red blood cells to detect anti-red blood cell autoantibody.
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Anemia, Hemolytic, Autoimmune↗
Theory of electrostatic effects in soft biological interfaces using atomic force microscopy.
We calculated the electrostatic force between a planar interface, such as a planar-supported lipid bilayer membrane, and the tip of a stylus on which another lipid bilayer or some other biomacromolecular system might be deposited. We considered styli with rounded tips as well as conical tips. To take into account the effect of dynamical hydrogen-bonded structures in the aqueous phase, we used a theory of nonlocal electrostatics. We used the Derjaguin approximation and identified the systems for which its use is valid. We pointed out where our approach differs from previous calculations and to what extent the latter are inadequate. We found that 1) the nonlocal interactions have significant effects over distances of 10-15 A from the polar zone and that, at the surface of this zone, the effect on the calculated force can be some orders of magnitude; 2) the lipid dipoles and charges are located a distance L from the hydrophobic layer in the aqueous medium and this can have consequences that may not be appreciated if it is ignored; 3) dipoles, located in the aqueous region, can give rise to forces even though the polar layer is unchanged, and if this is ignored the interpretation of force data can be erroneous if an attempt is made to rationalize an observed force with a knowledge of an uncharged surface; 4) the shape of the stylus tip can be very important, and a failure to take this into account can result in incorrect conclusions, a point made by other workers; and 5) when L is nonzero, the presence of charges and dipoles can yield a force that can be nonmonotonic as a function of ionic concentration.
Biophysical Phenomena↗
Combined atomic force microscopy and scanning tunneling microscopy imaging of cross-sectioned GaN light-emitting diodes.
Cross-sectional scanning tunneling microscopy (STM) was combined with atomic force microscopy (AFM) over the same area to characterize a cross-sectioned GaN light emitting diode. Because GaN is typically grown on a non-native substrate and also forms a wurtzite crystal structure, a cryogenic cleaving technique was developed to generate smooth surfaces. The depletion region surrounding the p-n junction was clearly identified using STM. Furthermore, by imaging under multiple sample biases, distinctions between the n-doped and p-doped GaN could be made.
Journal Article↗
Nanoscale characterization and determination of adhesion forces of Pseudomonas aeruginosa pili by using atomic force microscopy.
Type IV pili play an important role in bacterial adhesion, motility, and biofilm formation. Here we present high-resolution atomic force microscopy (AFM) images of type IV pili from Pseudomonas aeruginosa bacteria. An individual pilus ranges in length from 0.5 to 7 microm and has a diameter from 4 to 6 nm, although often, pili bundles in which the individual filaments differed in both length and diameter were seen. By attaching bacteria to AFM tips, it was possible to fasten the bacteria to mica surfaces by pili tethers. Force spectra of tethered pili gave rupture forces of 95 pN. The slopes of force curves close to the rupture force were nearly linear but showed little variation with pilus length. Furthermore, force curves could not be fitted with wormlike-chain polymer stretch models when using realistic persistence lengths for pili. The observation that the slopes near rupture did not depend on the pili length suggests that they do not represent elastic properties of the pili. It is possible that this region of the force curves is determined by an elastic element that is part of the bacterial wall, although further experiments are needed to confirm this.
Bacterial Adhesion↗
Basement membrane macromolecules: insights from atomic force microscopy.
The major macromolecules of basement membranes-collagen IV, laminin-1, and heparan sulfate proteoglycan (HSPG)-have been analyzed by atomic force microscopy (AFM), both individually and in combination with each other. The positions of laminin binding to collagen IV were mapped and compared with the positions of imperfections in the amino acid sequence of collagen IV; the apparent molecular volumes of the HSPG proteoglycans were measured and used to estimate the corresponding molecular weights. Even the thin, thread-like strands of the polyanion heparan sulfate can be visualized with AFM without staining, coating, or fixation. These strands are single polysaccharide chains and are thus thinner than single-stranded DNA. The heparan sulfate strands in HSPG are necessary for protein filtration in kidney basement membranes. We propose that these thin strands filter proteins by functioning as an entropic brush-i.e., that they filter proteins by their constant thermally driven motion in the basement membrane. These AFM analyses in air are a step toward AFM analyses under fluid of basement membrane macromolecules interacting with each other.
Animals↗
Direct atomic force microscopy visualization of integration host factor-induced DNA bending structure of the promoter regulatory region on the Pseudomonas TOL plasmid.
Atomic force microscopy (AFM) was used to analyze DNA bending induced by integration host factor (IHF). The direct AFM visualization of IHF-DNA complexes on the OP1 promoter regulatory regions on the Pseudomonas TOL plasmid showed that there was no intrinsic DNA bend in the OP1 promoter region, but a sharp DNA bend was induced by binding of IHF to the region between the upstream regulatory sequence and the promoter sequence. The DNA bending angles were distributed with a mean bend angle of 123 degrees. The IHF-DNA complexes were shown to bend at the IHF binding site giving rise to an asymmetric structure. These results provide direct evidence that IHF is required functionally for activation of OP1 transcription and support the DNA-loop model that the sharp DNA bend induced by binding of IHF facilitates the contact between RNA polymerase bound by the promoter sequence and XylR protein attached to the upstream sequence in the OP1 promoter.
Bacterial Proteins↗
Imaging biomolecule arrays by atomic force microscopy.
We describe here a method for constructing ordered molecular arrays and for detecting binding of biomolecules to these arrays using atomic force microscopy (AFM). These arrays simplify the discrimination of surface-bound biomolecules through the spatial control of ligand presentation. First, photolithography is used to spatially direct the synthesis of a matrix of biological ligands. A high-affinity binding partner is then applied to the matrix, which binds at locations defined by the ligand array. AFM is then used to detect the presence and organization of the high-affinity binding partner. Streptavidin-biotin arrays of 100 x 100 microns and 8 x 8 microns elements were fabricated by this method. Contact and noncontact AFM images reveal a dense lawn of streptavidin specific to the regions of biotin derivatization. These protein regions are characterized by a height profile of approximately 40 A over the base substrate with a 350-nm edge corresponding to the diffraction zone of the photolithography. High resolution scans reveal a granular topography dominated by 300 A diameter features. The ligand-bound protein can then be etched from the substrate using the AFM tip, leaving an 8 A shelf that probably corresponds to the underlying biotin layer.
Bacterial Proteins↗
Amplitude response of single-wall carbon nanotube probes during tapping mode atomic force microscopy: Modeling and experiment.
Imaging of surfaces with carbon nanotube probes in tapping mode results frequently in complex behavior in the amplitude-distance curves monitored. Using molecular mechanics simulations, we calculate the force exerted on a nanotube pressed against a smooth surface as it undergoes deformation and buckling. This nonlinear force is then used in a macroscopic equation, describing the response of a damped harmonic oscillator, to predict the amplitude response of a nanotube AFM probe. Similarities between the prediction and experiment suggest that the complex amplitude response seen in the experiment may be explained by the nonlinearity in the force exerted on the nanotube and thus must not necessarily be related to the structure of the surface.
Computer Simulation↗
The binding mode of the DNA bisintercalator luzopeptin investigated using atomic force microscopy.
The luzopeptins are DNA bisintercalating antibiotics that contain a decadepsipeptide to which are attached two quinoline chromophores. We have used atomic force microscopy (AFM) to investigate the interaction between luzopeptin B and DNA in an attempt to shed light on the binding mode of this antibiotic. AFM images provided contour lengths which were used as a direct measure of bisintercalation. Binding of luzopeptin B was investigated using two different DNA sequences, one having a GC content of 42% and the other 59%, which revealed a higher degree of bisintercalation into the DNA sequences having the lower GC content. The measured increment in contour length was found to plateau at values corresponding to binding of one drug molecule every 40 and 72 bp to the 42 and 59% GC sequences, respectively. In addition to the length increase, a higher proportion of DNA molecules displaying complex morphology was observed as the concentration of luzopeptin was increased. Such molecules were not included in the measurements of contour length. We propose that the various manifestations of complex morphology arise from both inter- and intramolecular cross-linking of the DNA caused by binding of luzopeptin, providing direct evidence of cross-linked species by AFM imaging.
Base Composition↗
Multilayer formation upon compression of surfactant monolayers depends on protein concentration as well as lipid composition. An atomic force microscopy study.
The determinants for the formation of multilayers upon compression of surfactant monolayers were investigated by compressing films, beyond the squeeze-out plateau, to a surface tension of 22 millinewtons/m. Atomic force microscopy was used to visualize the topography of lipid films containing varying amounts of native surfactant protein B (SP-B). These films were compared with films containing synthetic peptides based on the N terminus of human SP-B: monomeric mSP-B-(1-25) or dimeric dSP-B-(1-25). The formation of typical hexagonal network structures as well as the height of protrusions were shown to depend on the concentration of SP-B. Protrusions of bilayer height were formed from physiologically relevant concentrations of 0.2-0.4 mol % (4.5-8.5 wt %) SP-B upwards. Much higher concentrations of SP-B-(1-25) peptides were needed to obtain network structures, and protrusion heights were not equal to those found for films with native SP-B. A striking observation was that while protrusions formed in films of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/1,2-dipalmitoyl-sn-glycero-3-(phospho-rac-(1-glycerol)) (DPPG) (80/20) had single bilayer thickness, those formed in DPPC/1-palmitoyl-2-oleoyl-sn-glycero-3-(phospho-rac-(1-glycerol)) (80/20) had various heights of multilayers, whereas those seen in DPPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/DPPG (60/20/20) were mainly of bilayer height. For the first time direct observations by atomic force microscopy show (i) that a certain minimal concentration of SP-B is required for the formation of layered protrusions upon film compression, (ii) that protrusion height depends on whether the phospholipids contain an unsaturated fatty acyl chain, and (iii) that protrusion height also depends on whether the unsaturated acyl chain is present in phosphatidylcholine or in phosphatidylglycerol.
1,2-Dipalmitoylphosphatidylcholine↗