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Atsushi Ikai

Publications and source records attributed to Atsushi Ikai.

At least 19 recordsLinked to original sources
PubMed2006

Force profiles of protein pulling with or without cytoskeletal links studied by AFM.

To test the capability of the atomic force microscope for distinguishing membrane proteins with/without cytoskeletal associations, we studied the pull-out mechanics of lipid tethers from the red blood cell (RBC). When wheat germ agglutinin, a glycophorin A (GLA) specific lectin, was used to pull out tethers from RBC, characteristic force curves for tether elongation having a long plateau force were observed but without force peaks which are usually attributed to the forced unbinding of membrane components from the cytoskeleton. The result was in agreement with the reports that GLA is substantially free of cytoskeletal interactions. On the contrary, when the Band 3 specific lectin, concanavalin A, was used, the force peaks were indeed observed together with a plateau supporting its reported cytoskeletal association. Based on these observations, we postulate that the state of cytoskeletal association of particular membrane proteins can be identified from the force profiles of their pull-out mechanics.

Anion Exchange Protein 1, Erythrocyte↗
PubMed2006

Quantification of the number of EP3 receptors on a living CHO cell surface by the AFM.

The distribution of EP3 receptors on a living cell surface was quantitatively studied by atomic force microscopy (AFM). Green fluorescent protein (GFP) was introduced to the extracellular region of the EP3 receptor on a CHO cell. A microbead was used as a probe to ensure certain contact area, whose surface was coated with anti-GFP antibody. The interactions between the antibodies and GFP molecules on the cell surface were recorded to observe the distribution of the receptors. The result indicated that EP3 receptors were distributed on the CHO cell surface not uniformly but in small patches coincident with immunohistochemical observation. Repeated measurements on the same area of cell surface gave confirmation that it was unlikely that the receptors were extracted from the cell membrane during the experiments. The measurement of single molecular interaction between GFP and the anti-GFP antibody was succeeded on the cell surface using compression-free force spectroscopy. The value of separation work required to break a single molecular pair was estimated to be about 1.5 x 10(-18)J. The number of EP3 receptor on the CHO cell surface was estimated using this value to be about 1 x 10(4) under the assumption that the area of the cell surface was about 5,000 microm(2). These results indicated that the number of receptors on a living cell surface could be quantified through the force measurement by the AFM.

Animals↗
PubMed2006

AFM observation of immobilized self-oscillating polymer.

Various types of nanocomponents have been developed to construct a nanodevice or nanomachine. Here, we add a new nanocomponent that has the function of self-oscillation. A thermoresponsive polymer carrying a Ru complex, a catalyst of the Belousov-Zhabotinsky reaction, was synthesized and immobilized on a glass plate. Periodic turbidity changes in the aqueous solution of the polymer were observed, and nanoscale self-oscillation of the immobilized polymer was observed by a scanning probe microscope.

Catalysis↗
PubMed2006

Increased levels of granular tau oligomers: an early sign of brain aging and Alzheimer's disease.

Development of neurofibrillary tangles (NFTs) is a pathological hallmark in various neurodegenerative disorders including Alzheimer's disease (AD). Recently, we identified a granular tau oligomer having a pre-filamentous structure. To determine the role of this oligomer in NFT formation, we quantified the amount of granular tau oligomer in 21 frontal cortex samples, each displaying varying degrees of Braak-staged NFT pathology. Here we report that granular tau oligomer levels in frontal cortex were significantly increased, even in brains displaying Braak-stage I neuropathology, a stage at which clinical symptoms of AD and NFTs in frontal cortex are believed to be absent. This suggests that increases in granular tau oligomer levels occur before NFTs form and before individuals manifest clinical symptoms of AD. Increased granular tau oligomer levels, therefore, may lead to NFT formation in frontal cortex, eventually leading to the development of AD. Thus, increases in granular tau oligomer levels may represent a very early sign of NFT formation and AD.

Aged↗
PubMed2005

Local rigidity of a protein molecule.

Distribution of soft and rigid substructures within a protein molecule has been implicated in several occasions and most recently from the imaging and indentation experiments using an atomic force microscope. In this paper, previously reported result of mechanical extension experiments on the recombinant bovine carbonic anhydrase II, Q253C, is re-analyzed to estimate the distribution of Young's modulus, Y, in this protein. The force vs. extension curve of the enzymatically active, type I conformer gave an estimate of Y increasing from 40 to 220 MPa as the polypeptide chain was extended from 10 to 75 nm indicating the presence of a rigid core structure. The enzymatically inactive type II, in contrast, gave an almost constant modulus of 55+/-15 MPa in the same extension range in agreement with the previous proposal that it lacked a core structure.

Animals↗
PubMed2005

Pretransition and progressive softening of bovine carbonic anhydrase II as probed by single molecule atomic force microscopy.

To develop a simple method for probing the physical state of surface adsorbed proteins, we adopted the force curve mode of an atomic force microscope (AFM) to extract information on the mechanical properties of surface immobilized bovine carbonic anhydrase II under native conditions and in the course of guanidinium chloride-induced denaturation. A progressive increase in the population of individually softened molecules was probed under mildly to fully denaturing conditions. The use of the approach regime of force curves gave information regarding the height and rigidity of the molecule under compressive stress, whereas use of the retracting regime of the curves gave information about the tensile characteristics of the protein. The results showed that protein molecules at the beginning of the transition region possessed slightly more flattened and significantly more softened conformations compared with that of native molecules, but were still not fully denatured, in agreement with results based on solution studies. Thus the force curve mode of an AFM was shown to be sensitive enough to provide information concerning the different physical states of single molecules of globular proteins.

Animals↗
PubMed2004

Origin of mechanical strength of bovine carbonic anhydrase studied by molecular dynamics simulation.

The forced unfolding process of bovine carbonic anhydrase II (BCA II) was examined at the atomic level by the molecular dynamics (MD) simulation. By force spectroscopy, experimentally obtained force-extension curves (F-E curves) showed a prominent force peak after 50 nm extension. F-E curves obtained from our simulation had three force peaks appearing after extensions of 10-17 nm, 40 nm, and 53 nm, each signifying a brittle fracture of a specific local structure. Upon undergoing the final fracture at 53 nm of extension, the entire molecule became a single flexible chain and was further extended to its full theoretical length, almost as a random coil. This feature of the 53-nm peak strongly suggested its close correspondence to the experimentally observed force peak at approximately 60-nm extension. The 53-nm peak in the molecular dynamics simulation corresponded to the unfolding process of the beta-sheeted core that includes zinc-coordinating histidine residues. These results suggest that the structural change occurring at 50-60 nm in atomic force microscopy experiments corresponded to the destruction of the zinc coordination site.

Animals↗
PubMed2004

High sensitivity detection of protein molecules picked up on a probe of atomic force microscope based on the fluorescence detection by a total internal reflection fluorescence microscope.

We developed a method to detect and identify proteins on a probe of the atomic force microscope (AFM) with a high sensitivity. Due to a low background noise of the total internal reflection fluorescence microscope employed as a detecting system, we were able to achieve a high enough sensitivity to detect zeptomole orders of protein molecules immobilized on the tip. Several different methods to immobilize protein molecules to AFM-probes were tested, meant for a wide range of applications of this method. Furthermore, we demonstrated that different proteins were clearly distinguished by immunofluorescence microscopy on the probe using their specific antibodies.

Antibodies↗
PubMed2004

Fetal development of vomeronasal system in the goat.

Our previous study morphologically revealed that the adult goat vomeronasal (VN) system was different from the rodent and opossum one, and at least two types of VN systems exist in mammals. However, it remains unknown whether the developments in both types of VN systems are ontogenetically distinct and when the goat VN system is established. In this study, we morphologically observed the fetal development of the goat accessory olfactory bulb (AOB) and VN neuron. In the fetus, Gi2-expressing VN terminals terminated at glomeruli throughout the AOB, and no immunoreactivities for Go were detected in the nerve terminals reaching into AOB. The layer structure of AOB rapidly developed in the latter half of gestation. In the VN organ (VNO), at the middle stage of gestation, the dendritic processes of VN neuron were exposed in the VN lumen, and scattered and thin microvilli existed on the protrusion of the VN neuron. In the apical part of dendritic processes, no clear vesicle existed. However, the immunohistochemistry of an olfactory marker protein (OMP) revealed that a few VN neurons with OMP exist in VN sensory epithelium (VSE) before birth, although marked immunoreactivities were detected in adult VSE. Fetal VN neurons appeared to be underdeveloped. These results suggest that the goat VN system is ontogenetically distinct from the rodent and opossum VN systems, and is underdeveloped before birth. The goat VN system will develop and mature during the early postnatal period similar to the rodent and opossum VN systems.

Age Factors↗
PubMed2004

Structure of bovine carbonic anhydrase II at 1.95 A resolution.

Carbonic anhydrase (CA) is a zinc-containing enzyme that catalyzes the reversible hydration of CO2 to HCO3-. In eukaryotes, the enzyme plays a role in various physiological functions, including interconversion between CO2 and HCO3- in intermediary metabolism, facilitated diffusion of CO2, pH homeostasis and ion transport. The structure of bovine carbonic anhydrase II (BCA II) has been determined by molecular replacement and refined to 1.95 A resolution by simulated-annealing and individual B-factor refinement. The final R factor for the BCA II structure was 19.4%. BCA II has a C-terminal knot structure similar to that observed in human CA II. It contains one zinc ion in the active site coordinated to three histidines and one putative water molecule in a tetrahedral geometry. The structure of BCA II reveals a probable alternative proton-wire pathway that differs from that of HCA II.

Animals↗
PubMed2004

Dynamics of a partially stretched protein molecule studied using an atomic force microscope.

The dynamics of a single protein molecule subjected to forced mechanical unfolding was investigated in a millisecond time domain using a custom-made atomic force microscope (AFM) apparatus, which allows simultaneous measurements of an average tensile force applied to a single molecule and its mechanical response with respect to an external oscillation. Our target protein was genetically engineered bovine carbonic anhydrase II (BCA) which is a monomeric globular protein, and it has been shown that the as-expressed BCA from Escherichia coli contains two conformational isomers, one with enzymatic activity (type I) and the other without (type II). An interesting feature observed from the dynamic measurements was that when the type I BCA conformer was extended, it often exhibited a clear out-of-phase response against an external oscillation. The type II BCA conformer, however, always exhibited an in-phase response to the external oscillation. This relationship between different types of BCA and their dynamical behaviors was evidently observed around the discontinuous transition point from type I to II.

Animals↗
PubMed2004

Analysis of force curves obtained on the live cell membrane using chemically modified AFM probes.

Force curves were obtained on the live cell surface using an atomic force microscope mounted with a modified tip with the bifunctional covalent crosslinker, disuccinimidyl suberate, which forms a covalent bond with amino-bearing molecules on the cell surface. A ramp delay time of 1.0 s was introduced before the start of the retraction regime of the force curve to increase the stationary reaction time between the crosslinkers on the tip and the amino groups on the cell surface. While live cell surface responses to forced contact with a non-functionalized tip rarely showed evidence of tip-cell interaction, those obtained with modified tips gave clear indication of prolonged adhesion which was terminated by a single step release of the tip to its neutral position. Under the given experimental conditions of this work, 58% of a total of 198 force curves gave only one jump and 70% of those with one jump gave the final rupture force of 0.45+/0.22 [corrected] nN. The result emphasized the uniqueness of the observed mechanical response of the cell surface when probed with chemically modified tips.

Animals↗
PubMed2004

Quantitative measurement of mRNA at different loci within an individual living cell.

Asymmetric localizations of cellular proteins and mRNAs are important for cell functions such as division, differentiation and development. The localization of specific mRNA generates cell polarity by controlling the translation sites of specific proteins and thereby restricting their locations to appropriate cellular regions. We have previously reported a novel method based on atomic force microscopy (AFM) for examining gene expression in a single living cell without killing or destroying it. An AFM tip was inserted into a living cell to extract mRNAs, which were analyzed after multiplication by RT-PCR and quantitative PCR. By applying this method, in this study we performed quantitative measurement of mRNA at different loci within individual living cells.

Actins↗
PubMed2004

Quantitative analysis of the number of antigens immobilized on a glass surface by AFM.

To develop force measurements using an atomic force microscope (AFM) in a quantitative manner, it is necessary to estimate the number density of target molecules on a sample surface, and for this, the sensitivity of detection should be known. In this study, the AFM was used as a mechanical detector and an antigen and its antibody were used as a model to evaluate the sensitivity of detection. Antigens were immobilized on a glass surface and number density was estimated by monitoring optical absorbance due to product formation by the reaction of crosslinkers. The concentration of antigen was controlled by mixing control peptides. A microbead was used as a probe and antibodies were immobilized on the bead. AFM force measurements were then made for a range of number densities in the order of 10-10(6) antigen molecules per square micrometer of surface and were compared to evaluate the sensitivity of detection. Our result establishes the reliability of estimating a number of molecules like receptors on the cell surface, and indicates that the AFM is useful as a mechanical detector with high sensitivity.

Amino Acid Sequence↗
PubMed2003

Unfolding mechanics of multiple OspA substructures investigated with single molecule force spectroscopy.

We investigated mechanical unfolding of Borrelia burgdorferi outer surface protein A (OspA), a Lyme disease antigen containing a unique single-layer beta-sheet, with atomic force microscopy (AFM). We mechanically stretched a monomeric unit, rather than a tandem repeat, by pulling it from its N and C-terminal residues without using intervening polymer as a spacer. We detected two peaks in the force-extension profile before the final rupture of a fully extended polypeptide, which we interpreted as unfolding of multiple substructures in OspA. The double-peaked unfolding curves are consistent with results of previous thermodynamic studies showing two cooperative units in OspA. The mechanical unfolding processes were reversible, and the two substructures refolded within one second. Mutations near the boundary of the two thermodynamic cooperative units reduced the height of the first unfolding peak to undetectable levels and marginally affected the second one, indicating that the boundary between the two mechanical substructures is related to that previously assigned between the thermodynamic cooperative units. Based on a "worm-like chain" analysis of our AFM data, we propose a model for mechanical unfolding of OspA, where nearly a half of the chain is stretched with minimal resistive force, followed by sequential breakdown of C-terminal and N-terminal substructures. Based on these results, we discuss similarities and differences between mechanical and thermodynamic unfolding reactions of OspA. This work demonstrates that AFM study of monomeric proteins can elucidate details of the intramolecular mechanics of protein substructures.

Animals↗
PubMed2003

mRNA analysis of single living cells.

Analysis of specific gene expression in single living cells may become an important technique for cell biology. So far, no method has been available to detect mRNA in living cells without killing or destroying them. We have developed here a novel method to examine gene expression of living cells using an atomic force microscope (AFM). AFM tip was inserted into living cells to extract mRNAs. The obtained mRNAs were analyzed with RT-PCR, nested PCR, and quantitative PCR. This method enabled us to examine time-dependent gene expression of single living cells without serious damage to the cells.

Journal Article↗