Biomedical subjects
Publications and source records attributed to Masato Kodaka.
DNA-loaded microtubules (MTs) moving on a kinesin motor protein-coated substrate can selectively hybridize with a target fully matched DNA over single-base mismatched DNA and transport it. This technique is capable of collecting target biomolecules toward one point site to design new methodology of DNA analysis.
We have developed a novel mobile bioprobe using a conjugate of a kinesin-driven microtubule (MT) and malachite green (MG) as a platform for capturing MG RNA aptamers. The fluorescence of MG increases when it is bound to an MG aptamer, allowing MT-MG conjugates to work as sensors of RNA transcripts containing the MG aptamer sequence. Kinesin motor proteins provide an effective driving force to create mobile bioprobes without any manipulation. Although the fluorescence of a small number of MG-binding aptamers is low, the self-organization of tubulins into MTs enables the microscopic observation of the bound aptamers by collecting them on MTs. We demonstrate that MT-MG conjugates can select target aptamers from a transcription mixture and transport them without losing their inherent motility. Because the MG aptamer binds MG in a reversible manner, MT-MG conjugates can conditionally load and unload the target aptamers. This is one advantage of this system over the molecular probes developed previously in which reversible unloading is impossible due to high-affinity binding, such as between avidin and biotin. Furthermore, an MT-MG conjugate can be used as a platform for other MG aptameric sensors with recognition regions for various target analytes optimized by further selection procedures. This is the first step to applying living systems to in vitro devices. This technique could provide a new paradigm of mobile bioprobes establishing high-throughput in vitro selection systems using microfluidic devices operating in parallel.
Novel amphoteric particles are prepared by an interfacial polyaddition reaction of ethylene glycol diglycidyl ether (EGDGE) and L-lysine in a water-in-oil (W/O) miniemulsion system. The zeta-potential of the copolymer particle as a function of pH indicates a sigmoid curve with an isoelectric point at pH 8.7 due to the existence of secondary amino and carboxyl groups in the copolymer chain. The obtained amphoteric particle bears positive charge under pH 8.7 and negative charge over pH 8.7. This specific property of the pH-responsive amphoteric particle is employed to separate single-stranded DNA (ssDNA). The trapped ssDNA at pH 7.0 is almost released by changing pH to 11.0, which can be carried out repeatedly.
Nanoparticles comprising copolymers of aminoethylcarbamoyl-beta-cyclodextrin (AEC-beta-CD) and ethylene glycol diglycidyl ether (EGDGE) are prepared by an interfacial polyaddition reaction in a miniemulsion system. Polymers are formed in a W/O emulsion containing 0.25-10.0% (w/w) water and 5.0% (w/w) surfactant (MO-3S, tetraglycerin monoester, HLB 8.8), where simple particles are predominantly obtained when the water content is 1.0% and 5.0%. Notably, nano-size small particles (diameter: 0.3 microm) are formed under the condition of 5.0% water and 5.0% surfactant, which have the highest beta-CD contents (75.5 wt.%) and the most positive zeta-potential (53.6 mV). The zeta-potential measurement indicates that the obtained particles have positive charge due to protonation of their amino groups below around pH 10. Actually, uptake of 8-anilino-1-naphthalenesulfonic acid (ANS) bearing negative charge (SO(3)(-)) and moderate hydrophobicity depends on the magnitude of zeta-potential of the particles; viz., the particles with zeta-potential of 53.6 mV show the highest efficiency of uptake. The diameter and the beta-CD contents are closely related with the water/surfactant ratio, and the zeta-potentials are dependent on both the diameter and the beta-CD contents. Inclusion of ANS into the CD cavity of EGDGE/AEC-beta-CD particles can be controlled by electrostatic interaction between ANS (negatively charged) and the particle (positively charged). Namely, synergistic effect of cavity-inclusion and electrostatic interaction can dominate the uptake of guest molecules by the particles.
Metal complexes with GnRH were shown to interact with GnRH receptors in pituitary cells. In the present study we examined the effects of GnRH and its cobalt complex form (Co-GnRH) on LH secretion and generation of second messengers, namely inositol phosphates (IPs) and cAMP, in porcine pituitary cells in vitro. The cells were obtained from gilt pituitary at the pre-ovulatory phase of estrous cycle and cultured for 72 h before challenge with GnRH or Co-GnRH. Both substances induced a significant increase in LH release that was detectable after 60 min (P<0.05) of treatment, with the Co-GnRH complex being more efficient than GnRH at 180 min (P<0.01). GnRH and Co-GnRH were equally effective at 10(-8)M (P<0.01), however, at the lowest (10(-9)M) as well as the highest (10(-7)M) concentrations tested, Co-GnRH was more potent than its native counterpart (P<0.01). Interestingly, Co-GnRH revealed twice more efficient than GnRH at stimulating cAMP production, an effect which was detectable in cells after 1h-incubation (P<0.001). In contrast, while native GnRH induced a rapid increase (P<0.05) in IPs no such effect of Co-GnRH was observed. These data demonstrate that Co-GnRH and GnRH differentially effect on the signaling pathway in porcine gonadotropes and suggest that in these cells, the releasing action of Co-GnRH results from the mediation via the cAMP/protein kinase A second messenger system.
A new nano-biomachine has been created from microtubules (MTs) and hetero-bifunctional polymer particles bearing pyruvate kinase, which is propelled on glass surfaces coated with kinesin by use of self-supplying ATP.
MALDI-TOF mass spectrometry, 1H NMR spectrometry, the continuous variation method and molecular modeling by MM3 calculation confirmed our earlier studies showing that gonadotropin-releasing hormone (GnRH) forms complex with copper(II) ion with the binding ratio 1:1. The copper(II) complex formed at physiological pH has a square planar configuration and GnRH complexes with nickel(II) and cobalt(II) ions are less stable than that of copper(II).
Aggregation processes are analyzed by two kinetic models, the random polymerization model and the nucleation-dependent polymerization model. A kinetic equation for the random polymerization model can be derived analytically, revealing the relation between the initial monomer concentration ([M]0), the rate constant (k(a)), time (t), the yield of detectable aggregate ([F]), and the critical aggregation number (m). However, time-course curves for the nucleation-dependent polymerization model can be obtained by numerical calculation. It is found that lag time (t(d)) and half-time (t1/2) are proportional to [M](-1) in the random polymerization model, while t(d) and t1/2 are proportional to [M1](-s) (1 < s < n; n is nucleus size) at the lower concentration and are less dependent on [M1] at the higher concentration in the nucleation-dependent polymerization model.
Requirements for generating remarkable sigmoidal time-course of aggregation are found in the nucleation-dependent polymerization model by a numerical calculation method; i.e. there are optimum values of the kinetic constants to afford prominent sigmoidal character by inducing slightly unfavorable nucleation. However, if the nucleus formation is too unfavorable, sigmoidal character is again decreased. This result is in contrast to the generally accepted idea that sigmoid is induced by thermodynamically unfavorable nucleation phase.
Biotinylated and pyruvate kinase immobilized nano-bio element have been prepared using hetero-bifunctional latex beads, where the enzyme activity is roughly half of the free enzyme.
We design novel chromophoric amphiphiles 6a-c, which lead to pH-dependent membrane fusion of egg phosphatidylcholine (eggPC) liposome containing them. Lipids 6a-c comprise double alkyl chains, a single chain with a 2-nitrophenol group as a pH trigger, and dipeptide (Asp-Asp) between them. The pKa values of 2-nitrophenol groups of 6a-c in liposome are larger than that of hydrophilic compound 9 in an aqueous solution. Absorption spectra indicate that the fields around 2-nitrophenol of 6a-c situated in liposome membranes are more hydrophobic than that of 9 in an aqueous solution, whereas the environments around deprotonated 2-nitrophenolate of 6b and 6c are not so hydrophobic as that of 6a. This means that protonated 2-nitrophenol groups of 6a-c are embedded in bilayer membranes. Deprotonated 2-nitrophenol groups of 6b and 6c must be located in less hydrophobic circumstances, while that of 6a is still embedded in bilayer membranes because of its larger hydrophobicity. Absorption spectra and (1)H NMR spectra respectively suggest that protonated 2-nitrophenol groups of 6a and those of 6c might take face-to-face associations in bilayer membranes.
We have been using the B9/BM1 murine bone marrow metastasis model to study the function of adhesion molecules in the cell-cell interactions and transendothelial migration, necessary for tumor metastasis. The cell surface phenotype of these cells, which colonize vertebral and femoral marrow after intravenous injection, shows great similarity to that of human myeloma cells. In the present study, we investigated the interaction between B9/BM1 cells and osteoclasts, which likely support tumor metastasis in bone marrow. We found that co-culturing B9/BM1 cells and bone marrow-derived endothelial cells (BMECs) in the presence of vitamin D3 and M-CSF promoted differentiation of primary osteoclast progenitors to osteoclasts (detected by TRAP staining), and that this effect was blocked when BMECs were separated from the other cells by a porous polycarbonate membrane. Flow cytometry analysis showed that BMECs expressed RANKL (receptor activator of NF-kappaB ligand) protein on their surface, and that this expression was up-regulated by co-culture with B9/BM1 cells. Accordingly, RT-PCR showed expression of RANKL mRNA also to be up-regulated in BMECs co-cultured with B9/BM1 cells. Addition of OPG (osteoprotegerin, a decoy RANKL receptor) to the co-culture system completely blocked osteoclast induction, as did addition of anti-CD44 antibody. Furthermore, intravenous injection of B9/BM1 cells substantially increased the numbers of TRAP-positive osteoclasts detected in mice in vivo. Taken together, these findings suggest that B9/BM1 myeloma cells act via CD44 to stimulate RANKL expression on BMECs, which in turn physically interact with osteoclast progenitors to promote their differentiation to osteoclasts and metastasis in bone marrow.
Kinetic behavior of aggregation of amyloid-beta-protein (Abeta) is represented by a stretched exponential function, F=A[1-exp(-Bt(n))]. Differences in temperature-dependence of A, B and n are studied for Abeta 1-40 and Abeta 1-42. As the temperature is lowered, parameter A is increased, parameter B is decreased and parameter n is increased in Abeta 1-40, while these parameters are less sensitive to temperature in a more hydrophobic protein Abeta 1-42. ln B is a linear function of n, which is shown by ln B = -6.34n + 3.69.
We have developed a chemical method for directly identifying the amino acid residues of the transmembrane domain of a protein that are located right in the center of the membrane. Glycophorin A (GPA), the major sialoglycoprotein of human erythrocytes, was the first membrane protein whose primary sequence was elucidated, but its three-dimensional structure is still not known. GPA has been reconstituted into liposomes formed from dimyristoylphosphatidylcholine, dimyristoylphosphatidylserine, cholesterol, and a bola-amphiphilic phospholipidic photoactivatable probe (radioactive probe 1) by a detergent-mediated method. Electron microscopy confirmed the formation of spherical vesicular structures, and sucrose-density gradients revealed that the proteoliposomes comprised only one membrane fraction. Proteinase-K digestion of GPA in the proteoliposomes suggested that the orientation of GPA in reconstituted proteoliposomes was virtually identical to that observed in natural erythrocyte membranes. After photo-irradiation of the reconstituted proteoliposomes and in situ tryptic digestion, the photolabeled amino acid residues were analyzed by Edman degradation and their radioactivity was measured. Val80 and Met81, which had been assumed to be located near the center of the transmembrane domain of GPA, were indeed highly selectively photolabeled by probe 1. The new method might be applied to analyze the three-dimensional arrangement of the transmembrane domain of protein complexes that are made up from several subunits.
Beta-Amyloid peptide (Abeta) is the main protein components of neuritic plaques and its neurotoxicity would be exposed by formation of aggregate. The aggregation inhibitors composed of an Abeta recognition element (KLVFF) and a flexible hydrophilic disrupting element (aminoethoxy ethoxy acetate and aspartate) are designed and chemically synthesized. The inhibitory effects are examined by a pigment binding assay using Congo red or thioflavin T. The present compounds suppress the formation of aggregate, and the compound DDX3 is an especially effective inhibitor. In addition, the synthesized compounds efficiently suppress the cytotoxicity of Abeta against IMR-32 neuroblastoma cells in vitro.
Aspartic acid-derived artificial lipids (ADLs; s indicates the number of the methylene groups, s=2, 4, 6, 8, 10, 12) (Scheme 1) with various carboxyl alkyl chains as head groups are designed and synthesized, which are incorporated into liposome membranes by sonication. Fluorescence resonance energy transfer (FRET) measurements indicate that ADL6, ADL8 and ADL10 have high lipid-mixing ability in the acidic solution. The other ADLs, however, do not induce remarkable liposome fusion at acidic nor neutral pH. The hydrophobicity of the head groups of ADL6, ADL8 and ADL10 is suitable as triggers of membrane fusion.
A high-performance affinity purification technique has been developed for cisplatin (CDDP)-damaged DNA binding proteins directly from crude nuclear extracts of HeLaS3 cell using novel submicron beads synthesized by copolymerization of styrene and glycidyl methacrylate (GMA). The beads dramatically decreased both nonspecific protein adsorption on solid surfaces and elution volume and simplified the handling procedure. Preparation of the beads for purification was carried out by immobilization of telomeric repeats, (TTAGGG)(n), on the surface after the reaction with CDDP. At least nine proteins clearly showed higher affinity to CDDP-DNA and were identified by amino acid sequence analysis including HMGB (high mobility group), hUBF (human upstream binding factor), and Ku autoantigen, which were previously reported to be components of CDDP-damaged DNA binding proteins.