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K Akasaka

Publications and source records attributed to K Akasaka.

At least 37 records · Page 2Linked to original sources
PubMed2000

The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR.

The thermodynamic stability of staphylococcal nuclease was studied against the variation of both temperature and pressure by utilizing (1)H NMR spectroscopy at 750 MHz in 20 mM Mes buffer containing 99.9 % (2)H(2)O, pH 5.3. Equilibrium fractions of folded and unfolded protein species were evaluated with the proton signals of two histidine residues as monitor in the pressure range of 30-3300 bar and in the temperature range of 1.5 degrees C-35 degrees C. From the multi-parameter fit of the experimental data to the Gibbs energy equation expressed as a simultaneous function of pressure and temperature, we determined the compressibility change (Deltabeta), the volume change at 1 bar (DeltaV degrees ) and the expansivity change (Deltaalpha) upon unfolding among other thermodynamic parameters: Deltabeta=0.02(+/-0.003) ml mol(-1) bar(-1); Deltaalpha=1.33(+/-0.2) ml mol(-1) K(-1); DeltaV degrees =-41.9(+/-6. 3) ml mol(-1) (at 24 degrees C); DeltaG degrees =13.18(+/-2) kJ mol(-1) (at 24 degrees C); DeltaC(p)=13.12(+/-2) kJ mol(-1) K(-1); DeltaS degrees =0.32(+/-0.05) kJ mol(-1) K(-1 )(at 24 degrees C). The result yields a three-dimensional free energy surface, i.e. the free energy-landscape of staphylococcal nuclease on the P-T plane. The significantly positive Deltabeta and Deltaalpha values suggest that, in the pressure-denatured state, staphylococcal nuclease forms a loosely packed and fluctuating structure. The slight but statistically significant difference between the unfolding transitions of the His8 and His124 environments is considered to reflect local fluctuations in the native state, leading to pre-melting of the His124 environment prior to the cooperative unfolding of the major part of the protein.

Calorimetry↗
PubMed2000

Rapid internal dynamics of BPTI is insensitive to pressure. (15)N spin relaxation at 2 kbar.

Pressure effects on the backbone dynamics of a native basic pancreatic trypsin inhibitor (BPTI) have been measured by (15)N spin relaxation and chemical shifts at 30 and 2000 bar. The experiments utilized the on-line variable pressure cell nuclear magnetic resonance system on (15)N-uniformly labeled BPTI at a proton frequency of 750.13 MHz at 36 degrees C. Longitudinal (R(1)) and transverse (R(2)) (15)N relaxation times and ((1)H)-(15)N nuclear Overhauser effects were measured for 41 protonated backbone nitrogens at both pressures. The model free analysis of the internal dynamics gave order parameters for individual H-N vectors at both pressures. The results indicate that rapid internal dynamics in the ps-ns range for the polypeptide backbone is not significantly affected by pressure in the range between 30 bar and 2 kbar. The result is consistent with the linear pressure dependence of (1)H and (15)N chemical shifts of BPTI, which suggests that local compressibilities and amplitudes of associated conformational fluctuation are nearly invariant in the same pressure range. Overall, we conclude that at 2 kbar BPTI remains within the same native ensemble as at 1 bar, with a small shift of population from that at 1 bar.

Aprotinin↗
PubMed2000

Random PCR-based genome sequencing: a non-divide-and-conquer strategy.

We propose a genome sequencing strategy, which is neither divide-and-conquer (clone by clone) nor the shotgun approach. Random PCR-based and PCR relay sequencing constitute the basis of this novel strategy. Most of the genome is sequenced by the former process that requires only a set of non-specific primers and a template DNA. Random PCR-based sequencing reduces redundancy in sequencing by exploiting known sequence information. The number of primers required for random PCR was significantly diminished by using a combination of primers. The former process can be partially replaced by the shotgun method, if necessary. The gap-filling process can be effectively performed by way of PCR relay. The feasibility of this strategy was demonstrated using the Escherichia coli genome. This strategy enhances the global effort towards genome sequencing by being available through the Internet and by allowing the use of preexisting sequence data.

Base Sequence↗
PubMed2000

Evaluation of heterologous insulator function with regard to chromosomal position effect in the mouse blastocyst and fetus.

Insulators are located at the boundaries of differentially regulated genes and delimit their interactions by establishing independent chromatin structures. Recently, an insulator sequence has been found in the 5'-flanking region of arylsulfatase (ARS) gene from sea urchin. To investigate functional conservation of this ARS insulator in mice, we performed blastocyst assays to evaluate the effect of this insulator on the chromosomal position effect, quantitatively. We constructed transgenes that have a luciferase gene under the control of the CMV-IE enhancer and the human elongation factor 1 alpha promoter in the presence or absence of the ARS insulator in both flanking regions. These transgenes were microinjected into 1-cell mouse embryos and luciferase activity was measured at the blastocyst stage. We found that the presence of ARS insulator sequence doubled the number of luciferase-expressing blastocysts, and that the proportion of the blastocysts with high-level expression (> or = 1 x 10(4) relative light units (RLU)) was increased more than tenfold. In the case of transgenic fetuses, however, the presence of ARS insulator did not seem to improve transgene expression. These results suggest that the sea urchin ARS insulator confers position-independent expression driven by the human elongation factor 1 alpha promoter, at least in the blastocyst stage of the mouse.

Animals↗
PubMed2000

CAAT sites are required for the activation of the H. pulcherrimus Ars gene by Otx.

A product of sea urchin homologues of the Drosophila orthodenticle gene, HpOtxL has been implicated as a transcription activator of the aboral ectoderm-specific arylsulfatase (Ars) gene during early development of the sea urchin embryo. Using an in vivo transactivation system, we present evidence that HpOtxL activates the target gene by interacting with co-factors. Otx binding sites alone have little effect on the activity of an Ars promoter, but when both Otx binding sites and CAAT sequences are present in the enhancer region of Ars, the fragment shows a high enhancer activity. A gel mobility shift assay reveals that a nuclear protein binds to the CAAT sequences present near the Otx binding sites in the enhancer region of Ars. The activation domain of HpOtxL resides in the C terminal region between amino acids 218 and 238. The N-terminal region is responsible for the enhancement of transactivation of the Ars promoter, although the region itself does not function as an activation domain. HpOtxE, which possesses an N-terminal region different from HpOtxL, does not activate the Ars promoter even in the presence of CAAT sequences. Together with previous findings, our results suggest that Otx regulates different genes by interacting with different co-factors in sea urchin development.

Animals↗
PubMed2000

Relationship between EMG signals and force in human vastus lateralis muscle using multiple bipolar wire electrodes.

This paper describes the relationship between knee extension force and EMG signals detected by multiple bipolar wire electrodes inserted into the human vastus lateralis muscle under isometric conditions. Six healthy male volunteers participated in this study. Eight pairs of bipolar wire electrodes were inserted into the right vastus lateralis muscle and the EMG data were simultaneously detected and analyzed. The EMG raw data and individual force-IEMG relations were influenced by the location of the electrode inserted into the muscle. The force and IEMG relationship averaged across subjects detected from the eight electrodes, however, showed almost the same linear correlation in spite of different electrode locations. No linear correlation was observed between MdF and the knee extension force. This result suggests that, if all of the muscle fibers participate in the same action at the same time, the averaged normalized IEMG from any places using wire electrodes could reflect the total activities of that muscle even if the muscle is large.

Adult↗
PubMed2000

Pressure effect on the dynamics of an isolated alpha-helix studied by 15N-1H NMR relaxation.

Dynamics and structure of (1-36)bacteriorhodopsin solubilized in chloroform/methanol mixture (1:1) were investigated by 1H-15N NMR spectroscopy under a hydrostatic pressure of 2000 bar. It was shown that the peptide retains its spatial structure at high pressure. 15N transverse and longitudinal relaxation times, 15N[1H] nuclear Overhauser effects, chemical shifts and the translation diffusion rate of the peptide at 2000 bar were compared with the respective data at ambient pressure [Orekhov et al. (1999) J. Biomol. NMR, 14, 345-356]. The model free analysis of the relaxation data for the helical 9-31 fragment revealed that the high pressure decreases the overall rotation and translation diffusion, as well as apparent order parameters of fast picosecond internal motions (S2) but has no effect on internal nanosecond motions (S2 and taus) of the peptide. The decrease of translation and overall rotation diffusion was attributed to the increase in solvent viscosity and the decrease of apparent order parameters S2f to a compression of hydrogen bonds. It is suggested that this compression causes an elongation of H-N bonds and a decrease of absolute values of chemical shift anisotropy (CSA). In particular, the observed decrease of S2f at 2000 bar can be explained by 0.001 nm increase of N-H bond lengths and 10 ppm decrease of 15N CSA values.

Anisotropy↗
PubMed2000

Pressure alters electronic orbital overlap in hydrogen bonds.

Pressure-induced changes in 3hJ(NC') scalar couplings through hydrogen bonds were investigated in the immunoglobulin binding domain of streptococcal protein G. 1H, 15N and 13C triple-resonance NMR spectroscopy coupled with the on-line high pressure cell technique was used to monitor 3hJ(NC') scalar couplings at 30 and 2000 bar in uniformly labeled 15N and 13C protein isotopes. Both increased and decreased 3hJ(NC') scalar couplings were observed at high pressure. No correlation with secondary structure was apparent. The difference in coupling constants as well as pressure-induced chemical shift data suggests a compaction of the helix ends and an increase of the helix pitch at its center in response to pressure. Our data provides the first direct evidence that the electronic orbital overlap in protein backbone hydrogen bonds is altered by pressure.

Bacterial Proteins↗
PubMed2000

Pressure-induced local unfolding of the Ras binding domain of RalGDS.

The reliable prediction of the precise three-dimensional structure of proteins from their amino acid sequence is a major, still unresolved problem in biochemistry. Pressure is a parameter that controls folding/unfolding transitions of proteins through the volume change DeltaV of the protein-solvent system. By varying the pressure from 30 to 2,000 bar we detected using 15N/ 1H 2D NMR spectroscopy a unique equilibrium unfolding intermediate I in the Ras binding domain of the Ral guanine nucleotide dissociation stimulator (Ral GDS). It is characterized by a local melting of specific structural elements near hydrophobic cavities while the overall folded structure is maintained.

Binding Sites↗
PubMed2000

Sox regulates transcription of the sea urchin arylsulfatase gene.

A 50 bp region from -194 bp to -144 bp of the arylsulfatase gene (HpArs) of the sea urchin, Hemicentrotus pulcherrimus, is related to the temporally regulated expression of this gene. This region contains a Sox (Sry-related HMG box)-binding site, and the introduction of sequence mutations to this site significantly reduced the activity of the HpArs promoter, even in the presence of the C15 enhancer, which consists of HpOtx and CAAT motifs. A protein that binds to the Sox-binding site in the 50 bp region of the HpArs gene was detected in nuclear extracts of mesenchyme blastulae and a protein synthesized in vitro using SoxB1 cDNA of another sea urchin, Strongylocentrotus purpuratus, also bound to this Sox site. These results suggest that HpSox, which is maternally expressed and remains abundant by the pluteus stage, is clearly implicated in regulation of the HpArs gene. The presence of a negatively acting cis element in this 50 bp region has also been detected.

Animals↗
PubMed2000

15N and 1H NMR study of histidine containing protein (HPr) from Staphylococcus carnosus at high pressure.

The pressure-induced changes in 15N enriched HPr from Staphylococcus carnosus were investigated by two-dimensional (2D) heteronuclear NMR spectroscopy at pressures ranging from atmospheric pressure up to 200 MPa. The NMR experiments allowed the simultaneous observation of the backbone and side-chain amide protons and nitrogens. Most of the resonances shift downfield with increasing pressure indicating generalized pressure-induced conformational changes. The average pressure-induced shifts for amide protons and nitrogens are 0.285 ppm GPa(-1) at 278 K and 2.20 ppm GPa(-1), respectively. At 298 K the corresponding values are 0.275 and 2.41 ppm GPa(-1). Proton and nitrogen pressure coefficients show a significant but rather small correlation (0.31) if determined for all amide resonances. When restricting the analysis to amide groups in the beta-pleated sheet, the correlation between these coefficients is with 0.59 significantly higher. As already described for other proteins, the amide proton pressure coefficients are strongly correlated to the corresponding hydrogen bond distances, and thus are indicators for the pressure-induced changes of the hydrogen bond lengths. The nitrogen shift changes appear to sense other physical phenomena such as changes of the local backbone conformation as well. Interpretation of the pressure-induced shifts in terms of structural changes in the HPr protein suggests the following picture: the four-stranded beta-pleated sheet of HPr protein is the least compressible part of the structure showing only small pressure effects. The two long helices a and c show intermediary effects that could be explained by a higher compressibility and a concomitant bending of the helices. The largest pressure coefficients are found in the active center region around His15 and in the regulatory helix b which includes the phosphorylation site Ser46 for the HPr kinase. This suggests that this part of the structure occurs in a number of different structural states whose equilibrium populations are shifted by pressure. In contrast to the surrounding residues of the active center loop that show large pressure effects, Ile14 has a very small proton and nitrogen pressure coefficient. It could represent some kind of anchoring point of the active center loop that holds it in the right place in space, whereas other parts of the loop adapt themselves to changing external conditions.

Amides↗
PubMed2000

Structure of an analog of fusion peptide from hemagglutinin.

A 20-residue peptide E5 containing five glutamates, an analog of the fusion peptide of influenza virus hemagglutinin (HA) exhibiting fusion activity at acidic pH lower than 6.0-6.5 was studied by circular dichroism (CD), Fourier transform infrared, and 1H-NMR spectroscopy in water, water/trifluoroethanol (TFE) mixtures, dodecylphosphocholine (DPC) micelles, and phospholipid vesicles. E5 became structurally ordered at pH < or = 6 and the helical content in the peptide increased in the row: water < water/TFE < DPC approximately = phospholipid vesicle while the amount of beta-structure was approximately reverse. 1H-NMR data and line-broadening effect of 5-, 16-doxylstearates on proton resonances of DPC bound peptide showed E5 forms amphiphilic alpha-helix in residues 2-18, which is flexible in 11-18 part. The analysis of the proton chemical shifts of DPC bound and CD intensity at 220 nm of phospholipid bound E5 showed that the pH dependence of helical content is characterized by the same pKa approximately 5.6. Only Glu11 and Glu15 in DPC bound peptide showed such elevated pKas, presumably due to transient hydrogen bond(s) Glu11 (Glu15) deltaCOO- (H+)...HN Glu15 that dispose(s) the side chain of Glu11 (Glu15) residue(s) close to the micelle/water interface. These glutamates are present in the HA-fusion peptide and the experimental half-maximal pH of fusion for HA and E5 peptides is approximately 5.6. Therefore, a specific anchorage of these peptides onto membrane necessary for fusion is likely driven by the protonation of the carboxylate group of Glu11 (Glu15) residue(s) participating in transient hydrogen bond(s).

Circular Dichroism↗
PubMed2000

Absolute configuration of a ceramide with a novel branched-chain fatty acid isolated from the epiphytic dinoflagellate, Coolia monotis.

The absolute configuration of the chiral center at the C15 position of a novel branched-chain fatty acid derived from a new ceramide isolated from the epiphytic dinoflagellate Coolia monotis was determined to be of R from by reversed-phase HPLC after cleavage to 12-methylpentadecanoic acid and subsequent conversion with the chiral fluorescent reagent, (1R,2R)-2-(2,3-anthracenedicarboximido)cyclohexanol.

Animals↗
PubMed1999

KF25706, a novel oxime derivative of radicicol, exhibits in vivo antitumor activity via selective depletion of Hsp90 binding signaling molecules.

Radicicol, a macrocyclic antifungal antibiotic, has been shown to bind to the heat shock protein 90 (Hsp90) chaperone, interfering with its function. Hsp90 family chaperones have been shown to associate with several signaling molecules and play an essential role in signal transduction, which is important for tumor cell growth. Because radicicol lacks antitumor activity in vivo in experimental animal models, we examined the antitumor activity of a novel radicicol oxime derivative, radicicol 6-oxime (KF25706), on human tumor cell growth both in vitro and in vivo. KF25706 showed potent antiproliferative activities against various human tumor cell lines in vitro and inhibited v-src- and K-ras-activated signaling as well as radicicol. In addition, Hsp90 family chaperone-associated proteins, such as p185erbB2, Raf-1, cyclin-dependent kinase 4, and mutant p53, were depleted by KF25706 at a dose comparable to that required for antiproliferative activity. KF25706 was also shown to compete with geldanamycin for binding to Hsp90. KF29163, which is an inactive derivative of radicicol, was less potent both in p185erbB2 depletion and Hsp90 binding. More importantly, KF25706 showed significant growth-inhibitory activity against human breast carcinoma MX-1 cells transplanted into nude mice at a dose of 100 mg/kg twice daily for five consecutive i.v. injections. KF25706 was also shown to possess antitumor activity against human breast carcinoma MCF-7, colon carcinoma DLD-1, and vulval carcinoma A431 cell lines in vivo in an animal model. Finally, we confirmed the depletion of Hsp90-associated signaling molecules (Raf-1 and cyclin-dependent kinase 4) with ex vivo Western blotting analysis using MX-1 xenografts. In agreement with in vivo antitumor activity, KF25706 depleted Hsp90-associated molecules in vivo, whereas KF29163 and radicicol did not show this activity in vivo. Taken together, these results suggest that antitumor activity of KF25706 may be mediated, at least in part, by binding to Hsp90 family proteins and destabilization of Hsp90-associated signaling molecules.

Animals↗