Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “atomic force microscopy”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67Linked to original sources
PubMed2004

Preliminary studies of the 2D crystallization of Omp1 of Serratia marcescens: observation by atomic force microscopy in native membranes environment and reconstituted in proteolipid sheets.

In this work the porin Omp1 of Serratia marcescens was expressed in a porin deficient mutant (Escherichia coli UH302) and its functionality studied following the accumulation of ciprofloxacin in bacteria. The protein was extracted, purified and reconstituted in proteoliposomes of different composition (lipopolysaccharide (LPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)). Maximum extraction of the detergent was achieved applying different steps of dialysis and centrifugation. Proteolipid sheets with different composition were spread onto mica and observed by atomic force microscopy. Two-dimensional crystal of Omp1 was not observed in any case due to low resolution achieved. Judging from the images features POPC is the most suitable phospholipid to enhance 2D lattice formation for Omp1.

Anti-Infective Agents↗
PubMed2006

Solubilization of supported lipid membranes by octyl glucoside observed by time-lapse atomic force microscopy.

Detergents are very useful for the purification of membrane proteins. A good detergent for protein extraction has to prevent denaturation by unfolding, and to avoid aggregation. Therefore, gaining access to the mechanism of biomembranes' solubilization by detergents is crucial in biochemical research. Among the wide range of detergents used to purify membrane proteins, n-octyl beta-D-glucopyranoside (OG) is one of the most important as it can be easily removed from final protein extracts. Here, we used real-time atomic force microscopy (AFM) imaging to visualize the behavior of a model supported lipid bilayer in the presence of OG. Two kinds of supported model membranes were prepared by fusion of unilamellar vesicles: with an equimolar mixing of dioleoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DOPC/DPPC) or with DPPC alone. Time-lapse AFM experiments evidenced that below its critical micelle concentration (CMC), OG was not able to solubilize the bilayer but the gel DPPC domains were instantly dissolved into the DOPC matrix. This result was interpreted as a disorganization of the DPPC molecular packing induced by OG. When membranes were incubated with OG at concentrations higher than CMC, the detergent immediately provoked the complete and immediate desorption of the whole bilayer for both compositions: DPPC and DOPC/DPPC. After a while, some patches appeared onto the bare mica surface. This redeposition activity, together with fusion events, progressively led to the recovery of a continuous bilayer. These results provide a new insight on the unique properties of OG employed in membrane reconstitution protocols.

1,2-Dipalmitoylphosphatidylcholine↗
PubMedDate not supplied

Use of phase imaging in atomic force microscopy for measurement of viscoelastic contrast in polymer nanocomposites and molecularly thick lubricant films.

Phase contrast microscopy, using an atomic force microscope, is used to detect and quantify changes in composition across polymer nanocomposites and molecularly thick lubricated surfaces. The technique takes advantage of the contrast in viscoelastic (viscous energy dissipation) properties of the different materials across the surface. Some materials, especially polymers, are found to display viscoelastic behavior. For such materials, the strain response lags the stress by a phase angle that is characteristic of the material. In tapping (or intermittent contact) mode, phase angle contrast is found to be highly dependent on vibration amplitude and mean tip-to-sample distance (setpoint). Phase angle contrast seems to be a stronger function of viscoelastic properties at relatively high vibration amplitude and low mean tip-to-sample distance. In this regime the effects of sample deformation, and thus viscoelastic properties, are dominant. In these contrast images, low phase angle corresponds to materials with low viscoelastic properties. This technique was used to find fairly reproducible phase angle contrast for polyethylene terephthalate (PET) films with embedded ceramic particles, metal particle (MP) magnetic tape, and Si(100) with a nonuniform Z-15 lubricant film. Very little correlation is found between phase angle images and friction force images for PET films with embedded ceramic particles and MP tape; phase angle images give information that cannot be obtained from topography or friction images. A numerical vibration model verifies that viscoelastic properties are dominant for high vibration amplitude and low mean tip-to-sample distance. For these conditions, the model also verifies that low phase angle corresponds to low viscoelastic properties.

Journal Article↗
PubMed2005

Membrane deformation of unfixed erythrocytes in air with time lapse investigated by tapping mode atomic force microscopy.

Estimation of the time of death is one of the most important problems for forensic medicine and law. Physical and chemical postmortem changes are evaluated together while estimating the time of death. The pattern analysis of antemortem and postmortem bloodstains is one of the important parameters for forensic science, and cellular changes of blood cells can be useful for the quantitative assessment of the time of death. In this study, by successively investigating erythrocytes exposed in air on mica for 5 days using tapping mode atomic force microscopy (TM-AFM), we observed deformation of whole cell and membrane surface of unfixed erythrocytes with time lapse. We found that the time-dependent cellular changes occurred after exposure of erythrocytes in air for several days. At 0.5 days of exposure, fissures and cell shrinkage were observed. At 2.5 days of exposure, the emergence of nanometer-scale protuberances were observed and these protuberances increased in number with increasing time. The changes of cell shape and cell membrane surface ultrastructure can be used to estimate the time of death. Futhermore, smear-induced abnormal erythrocytes and immunostained erythrocytes were observed here. The need for more precise research is indicated, such as the correlation of membrane changes to intervals of less than 0.5 day of air exposure, and use of various substrates in addition to mica, including glass, metals, fabrics, among others, on which the bloodstains appear in crime scenes. The results of this research demonstrate the efficacy of AFM as a potentially powerful analytical tool in forensic science.

Air↗
PubMed2006

Dynamic adhesion of T lymphocytes to endothelial cells revealed by atomic force microscopy.

The recruitment of T lymphocytes to lymphoid organs or sites of inflammation is a crucial step in adaptive immunity. These processes require endothelial activation and expression of adhesion molecules, including E- and P-selectins, intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). However, the complete characterization of the adhesion strength and dynamics between lymphocytes and endothelial cells has been hampered by the lack of sensitive quantitative techniques. Here we report on the application of atomic force microscopy to characterize the interaction between individual pairs of living T lymphocytes (i.e., Jurkat cells) and human umbilical vein endothelial cells (HUVECs). The detachment of individual cell-cell conjugates was a complex process involving several step-like rupture events and the viscoelastic deformation of cells on the scale of several microns. Adhesion between Jurkat cells and activated endothelial cells increased with compression force and contact time, with the most dramatic changes occurring within the first half second of contact. After 0.25 sec of contact, E-selectin, ICAM-1, and VCAM-1 contributed to 18%, 39%, and 41% of total adhesion strength, respectively, suggesting that ICAM-1 and VCAM-1 contributed more than the selectins in supporting cell attachment.

Cell Adhesion↗
PubMed2005

Preservation of bone collagen from the late Cretaceous period studied by immunological techniques and atomic force microscopy.

Late Cretaceous avian bone tissues from Argentina demonstrate exceptional preservation. Skeletal elements are preserved in partial articulation and suspended in three dimensions in a medium-grained sandstone matrix, indicating unusual perimortem taphonomic conditions. Preservation extends to the microstructural and molecular levels. Bone tissues respond to collagenase digestion and histochemical stains. In situ immunohistochemistry localizes binding sites for avian collagen antibodies in fossil tissues. Immunohistochemical studies do not, however, guarantee the preservation of molecular integrity. A protein may retain sufficient antigenicity for antibody binding even though degradation may render it incapable of original function. Therefore, we have applied atomic force microscopy to address the integrity and functionality of retained organic structures. Collagen pull-off measurements not only support immunochemical evidence for collagen preservation for antibody recognition but also imply preservation of the whole molecular integrity. No appreciable differences in collagen pull-off properties were measured between fossil and extant bone samples under physiological conditions.

Animals↗
PubMed2004

The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus.

The clamp-loader-helicase interaction is an important feature of the replisome. Although significant biochemical and structural work has been carried out on the clamp-loader-clamp-DNA polymerase alpha interactions in Escherichia coli, the clamp-loader-helicase interaction is poorly understood by comparison. The tau subunit of the clamp-loader mediates the interaction with DnaB. We have recently characterised this interaction in the Bacillus system and established a tau(5)-DnaB(6) stoichiometry. Here, we have obtained atomic force microscopy images of the tau-DnaB complex that reveal the first structural insight into its architecture. We show that despite the reported absence of the shorter gamma version in Bacillus, tau has a domain organisation similar to its E.coli counterpart and possesses an equivalent C-terminal domain that interacts with DnaB. The interaction interface of DnaB is also localised in its C-terminal domain. The combined data contribute towards our understanding of the bacterial replisome.

Adenosine Triphosphatases↗
PubMed2006

Characterization of a single molecular QCA cell by Q-control enhanced amplitude modulation atomic force microscopy.

Major technical challenges for reduction of device sizes for computation and memory are the interconnection and power dissipation problems. Molecular quantum-dot cellular automata (QCA) have been proposed as solutions to this problem. Silicon phthalocyanine (SiPc) is a possible candidate for a molecular QCA element. Therefore, it is important to develop an in situ observation technique to visualize individual SiPc molecules. We report here the first image of a single SiPc dimer in air by using quality factor control (Q-control) enhanced amplitude modulation atomic force microscopy (AFM) and an investigation of the interaction forces between the tip and SiPc dimer. The AFM was operated at 0% relative humidity in an ultrapure nitrogen environment either with or without Q-control. Theoretical simulations using the point-mass description of the AFM, demonstrated that Q-enhancement reduced the force exerted from the tip to the sample surface. Our results, consistent with theory, demonstrated that the image force was reduced and a greater height and a larger size were measured. The advantages of this method can be extended to the AFM observation of other "soft" structures, and these results can be useful for a wider community.

Computers, Molecular↗
PubMed2005

Early events in insulin fibrillization studied by time-lapse atomic force microscopy.

The importance of understanding the mechanism of protein aggregation into insoluble amyloid fibrils lies not only in its medical consequences, but also in its more basic properties of self-organization. The discovery that a large number of uncorrelated proteins can form, under proper conditions, structurally similar fibrils has suggested that the underlying mechanism is a general feature of polypeptide chains. In this work, we address the early events preceding amyloid fibril formation in solutions of zinc-free human insulin incubated at low pH and high temperature. Here, we show by time-lapse atomic force microscopy that a steady-state distribution of protein oligomers with a quasiexponential tail is reached within a few minutes after heating. This metastable phase lasts for a few hours, until fibrillar aggregates are observable. Although for such complex systems different aggregation mechanisms can occur simultaneously, our results indicate that the prefibrillar phase is mainly controlled by a simple coagulation-evaporation kinetic mechanism, in which concentration acts as a critical parameter. These experimental facts, along with the kinetic model used, suggest a critical role for thermal concentration fluctuations in the process of fibril nucleation.

Amyloid↗
PubMed2000

Imaging and mapping heparin-binding sites on single fibronectin molecules with atomic force microscopy.

Fibronectin is composed of multiple homologous repeats and contains many functional domains. Two major heparin-binding domains have previously been identified: the Hep I site near the amino terminus and the Hep II site near the carboxyl terminus. The Hep II site has been considered the high-affinity heparin-binding site based on studies of fibronectin fragments. However, few studies have been carried out on heparin binding by intact fibronectin. We imaged single fibronectin molecules as well as heparin-coated gold particles bound to whole dimeric plasma fibronectin molecules with tapping mode atomic force microscopy. We observed heparin-gold particles preferentially bound at two locations that correspond to the Hep I and Hep II sites. Quantitative analysis of images of individual fibronectin-heparin-gold complexes showed that almost twice as many heparin-gold particles bound to the N-terminal Hep I site compared to the Hep II site. In contrast to previous findings with fibronectin fragments, these results suggest that the Hep I site has a binding affinity higher than or comparable to the Hep II site in the intact fibronectin molecule.

Animals↗
PubMed2006

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.

Animals↗
PubMed2005

Atomic force microscopy reveals the stoichiometry and subunit arrangement of 5-HT3 receptors.

The 5-HT3 receptor is a cation-selective ligand-gated ion channel of the Cys-loop superfamily. The receptor is an important therapeutic target, with receptor antagonists being widely used as antiemetics in cancer therapy. The two known receptor subunits, A and B, form homomeric 5-HT 3A receptors and heteromeric 5-HT 3A/B receptors. The heteromeric receptor has the higher single-channel conductance and more closely mimics the properties of the native receptor. We have used atomic force microscopy to study the architecture of 5-HT 3A and 5-HT 3A/B receptors. We engineered different epitope tags onto the A- and B-subunits and imaged receptors that were doubly liganded by anti-epitope antibodies. We found that, for the 5-HT 3A/B receptor, the distribution of angles between antibodies against the A-subunit had a single peak at approximately 144 degrees , whereas the distribution for antibodies against the B-subunit had two peaks at approximately 72 degrees and 144 degrees . Our results indicate that the subunit stoichiometry is 2A:3B and that the subunit arrangement around the receptor rosette is B-B-A-B-A. This arrangement may account for the difference between the agonist Hill coefficients and the single-channel conductances for the two types of receptor.

Animals↗
PubMed2000

Atomic force microscopy reveals two conformations of the 20 S proteasome from fission yeast.

The proteasome is a major cytosolic proteolytic complex, indispensable in eukaryotic cells. The barrel-shaped core of this enzyme, the 20 S proteasome, is built from 28 subunits forming four stacked rings. The two inner beta-rings harbor active centers, whereas the two outer alpha-rings play a structural role. Crystal structure of the yeast 20 S particle showed that the entrance to the central channel was sealed. Because of this result, the path of substrates into the catalytic chamber has remained enigmatic. We have used tapping mode atomic force microscopy (AFM) in liquid to address the dynamic aspects of the 20 S proteasomes from fission yeast. We present here evidence that, when observed with AFM, the proteasome particles in top view position have either open or closed entrance to the central channel. The preferred conformation depends on the ligands present. Apparently, the addition of a substrate to the uninhibited proteasome shifts the equilibrium toward the open conformation. These results shed new light on the possible path of the substrate into the proteolytic chamber.

Cysteine Endopeptidases↗
PubMed1996

Atomic force microscopy visualizes ATP-dependent dissociation of multimeric TATA-binding protein before translocation into the cell nucleus.

The TATA-binding protein (TBP) is a universal transcription factor which plays an essential role in eukaryotic gene expression. As a karyophilic molecule, this cytosolic protein reaches its DNA-binding site through the transport channel of the nuclear pore complex. As occurs with other major cellular proteins, TBP forms multimers in solution, which is a limiting factor for nuclear translocation. While studying the nuclear translocation of TBP, we detected ATP-dependent multimerization of TBP with atomic force microscopy. In physiological solutions containing ATP, 14-molecule multimers dissociated into four-molecule multimers with a half-maximum dissociation constant of 10 microM. Electrophysiological experiments using isolated cell nuclei of cultured kidney cells revealed that TBP translocates into the cell nucleus only in the presence of ATP. When ATP was replaced with its slowly hydrolysing analogue, ATP[gamma-S] [i.e. adenosine 5'-o-(3-thiotriphosphate)], the aggregates remained intact and nuclear translocation was not possible. Taken together, our investigations suggest that TBP exhibits ATPase activity similar to that observed in relation to molecular chaperons. This activity secures physiological translocation of the transcription factor into the nucleus.

Adenosine Triphosphate↗
PubMed2003

The ring structure and organization of light harvesting 2 complexes in a reconstituted lipid bilayer, resolved by atomic force microscopy.

The main function of the transmembrane light-harvesting complexes in photosynthetic organisms is the absorption of a light quantum and its subsequent rapid transfer to a reaction center where a charge separation occurs. A combination of freeze-thaw and dialysis methods were used to reconstitute the detergent-solubilized Light Harvesting 2 complex (LH2) of the purple bacterium Rhodopseudomonas acidophila strain 10050 into preformed egg phosphatidylcholine liposomes, without the need for extra chemical agents. The LH2-containing liposomes opened up to a flat bilayer, which were imaged with tapping and contact mode atomic force microscopy under ambient and physiological conditions, respectively. The LH2 complexes were packed in quasicrystalline domains. The endoplasmic and periplasmic sides of the LH2 complexes could be distinguished by the difference in height of the protrusions from the lipid bilayer. The results indicate that the complexes entered in intact liposomes. In addition, it was observed that the most hydrophilic side, the periplasmic, enters first in the membrane. In contact mode the molecular structure of the periplasmic side of the transmembrane pigment-protein complex was observed. Using Föster's theory for describing the distance dependent energy transfer, we estimate the dipole strength for energy transfer between two neighboring LH2s, based on the architecture of the imaged unit cell.

Crystallography↗
PubMed1998

A quantitative study of optical mapping surfaces by atomic force microscopy and restriction endonuclease digestion assays.

Many new techniques in biomolecular chemistry and genomic analysis require the immobilization of molecular reagents on specially prepared surfaces. However, the process of molecular fixation often interferes with or precludes the use of standard in vitro biochemical assays. Optical mapping is an emergent technology for genomic analysis which relies on the biochemical activity of DNA fixed to silanized glass surfaces. Optical mapping surfaces have been shown to be compatible with restriction endonucleases and a variety of DNA polymerases. The essential properties of biochemically active surfaces are poorly understood in most of the current technologies which utilize molecular fixation, including optical mapping. The purpose of this study is to use the powerful technique of atomic force microscopy, in combination with informative enzymatic assays, to correlate biochemical activity with microscopic surface structure. The results presented provide meaningful insight into the effect of surface preparation on the biochemical accessibility of surface-bound molecules. Novel analysis which may facilitate the automation of optical mapping is presented.

DNA↗
PubMed2000

Nuclear pores collapse in response to CO2 imaged with atomic force microscopy.

Nuclear pore complexes (NPCs) are the rate-limiting barriers for the exchange of macromolecules (e.g. transcription factors or mRNA) between the nuclear and cytosolic compartments. NPC conformation determines movement of cargo in either direction and thus controls gene expression. ATP and calcium are known to induce an NPC shape change (increase in height and decrease in diameter) indicating pore contraction. Here we report a CO2-induced shape change which is different to the ATP/calcium response. Experiments were performed on the isolated nuclear envelope of Xenopus laevis oocytes. The nuclear envelope was spread on glass and the native cytoplasmic surface was imaged with atomic force microscopy (AFM). The preparation was scanned in a water-saturated 100% O2 atmosphere at room temperature. Exposure to 5% CO2 (95%O2) led over a time course of minutes to a dramatic NPC shape change (decrease in height and decrease in diameter) indicating pore closure. NPCs turned flat and central channel openings virtually disappeared. The CO2 response was only slowly reversible. We conclude that NPCs apparently collapse in response to CO2, a structural change that could lead to the functional isolation of the cell nucleus.

Adenosine Triphosphate↗
PubMed2000

Tapping-mode atomic force microscopy on intact cells: optimal adjustment of tapping conditions by using the deflection signal.

Difficulties in the proper adjustment of the scanning parameters are often encountered when using tapping-mode atomic force microscopy (TMAFM) for imaging thick and soft material, and particularly living cells, in aqueous buffer. A simple procedure that drastically enhances the successful imaging of the surface of intact cells by TMAFM is described. It is based on the observation, in liquid, of a deflection signal, concomitant with the damping of the amplitude that can be followed by amplitude-distance curves. For intact cells, the evolution of the deflection signal, steeper than the amplitude damping allows a precise adjustment of the feedback value. Besides its use in finding the appropriate tapping conditions, the deflection signal provides images of living cells that essentially reveal the organization of the membrane cytoskeleton. This allows to show that changes in the membrane surface topography are associated with a reorganization of the membrane skeleton. Studies on the relationships between the cell surface topography and membrane skeleton organization in living cells open a new field of applications for the atomic force microscope.

Animals↗