All-polarization-maintaining Er-doped ultrashort-pulse fiber laser using carbon nanotube saturable absorber.

We present an all-polarization-maintaining Er-doped ultrashort-pulse fiber laser using a single-wall carbon nanotube polyimide nanocomposite saturable absorber. The maximum average power for single-pulse operation is 4.8 mW, and the repetition frequency is 41.3 MHz. Self-start and stable mode-locking operation is achieved. The RF amplitude noise is also examined and it is confirmed that the noise figure is as low as that of a solid-state laser. Using a polarization-maintaining anomalous dispersive fiber, a 314 fs output pulse is compressed to 107 fs via higher-order soliton compression. The peak power of the compressed pulse is up to 1.1 kW.

Detection and expression of a gene encoding a new bacteriorhodopsin from an extreme halophile strain HT (JCM 9743) which does not possess bacteriorhodopsin activity.

Membrane vesicles prepared from an extreme halophile strain, HT (JCM 9743), showed no bacteriorhodopsin activity. However, a DNA fragment, amplified by polymerase chain reaction (PCR), appeared to encode the C to G helices of a bacteriorhodopsin (bR)-like protein. With the PCR product as a probe, the gene coding for a novel bacteriorhodopsin was cloned from the genomic DNA of the strain HT. The open reading frame of the gene was ligated with the promoter region of the bop gene of Halobacterium salinarum bR, and expressed in a bR-deficient host strain, L33, using the plasmid vector pXLNov-R. The purplish membrane fraction purified from cells of a transformant exhibited a cyclic photoreaction characteristic of bacteriorhodopsin.

Halolysin R4, a serine proteinase from the halophilic archaeon Haloferax mediterranei; gene cloning, expression and structural studies.

A gene encoding a halophilic serine proteinase, halolysin R4, from a halophilic archaeon Haloferax mediterranei strain R4 was cloned, its nucleotide sequence determined, and expressed in Haloferax volcanii WFD11. The deduced amino-acid sequence (403 aa in length) showed the highest similarity to halolysin 172P1, produced by another halophilic archaeon, strain 172P1 (now designated as Natrialba asiatica). Both halolysins belong to the thermitase branch of class I subtilases, but show long C-terminal extensions of 117 and 123 amino acids, respectively. Removal of this "tail' region from halolysin R4 abolished proteinase activity, indicating it provides an essential (but as yet unknown) function. Substitution of the two cysteine residues in the C-terminal extension with serine decreased enzyme stability in hypotonic solutions, possibly owing to disruption of potential disulfide bonds or perturbation of calcium binding site(s).

Conformational deformation in deoxymyoglobin by hydrostatic pressure.

Pressure effect on the equilibrium conformation in sperm whale deoxymyoglobin and its volume fluctuation are studied by the normal mode analysis and strain tensor analysis. The pressure-induced deformation of interhelix regions are found to be remarkably more compressed than the other parts of the molecule. The intrahelix compressibility is shown to be relatively small. We also calculate the compressibility of the three hydrophobic clusters, located at the bottom, distal, and proximal side of the heme. Its value is found to decrease in the indicated order. The average compressibility of these hydrophobic clusters is less than the average interhelix compressibility, even though there are large cavities in these clusters. In order to study overall deformation, we define a linear compressibility and calculate it for all pairs of C alpha atoms. The pressure-induced deformation is observed to be heterogeneous also in this analysis. The calculated root-mean-square displacement of the constituent atoms in the equilibrium conformation at 1,000 atm from those at 0 atm is 0.12 A, which is much smaller in magnitude than the average value of the atomic fluctuations at room temperature. In the water solvent, the volume excluded by the protein molecule in the equilibrium conformation is reduced by 0.9%, when the pressure is raised from 0 to 1,000 atm. The calculated magnitude of the root-mean-square volume fluctuation is 0.3% of the excluded volume at room temperature. The square of the volume fluctuation is given as a sum of contributions from individual normal modes. Contributions from low frequency normal modes are found to dominate over those from higher frequency normal modes. The estimated value of the isothermal compressibility of deoxymyoglobin is 9.37 x 10(-12) cm2/dyn.

Partial sequence of the gene for a serine protease from a halophilic archaeum Haloferax mediterranei R4, and nucleotide sequences of 16S rRNA encoding genes from several halophilic archaea.

A part of the gene coding for a halophilic serine protease from a halophilic archaeum Haloferax mediterranei R4 was amplified by PCR and its 672 nucleotide sequence was determined. Tentative translation to the amino acid sequence suggested that the enzyme was quite similar to halolysin produced by another halophilic archaeum strain 172P1. Nucleotide sequences of 16S rRNA encoding genes from 9 halophilic archaea were determined. Alignment of 19 sequences known so far showed that there are more than 20 positions carrying bases or deletions specific for each halobacterial genus: Halobacterium, Haloarcula, Haloferax, and Halococcus.

Molecular cloning and sequencing of the gene for a halophilic alkaline serine protease (halolysin) from an unidentified halophilic archaea strain (172P1) and expression of the gene in Haloferax volcanii.

The gene of a halophilic alkaline serine protease, halolysin, from an unidentified halophilic archaea (archaebacterium) was cloned and its nucleotide sequence was determined. The deduced amino acid sequence showed that halolysin consists of 411 amino acids, with a molecular weight of 41,963. The highest homology was found with thermitase from Thermoactinomyces vulgaris. Halolysin has a long C-terminal extension of approximately 120 amino acids which has not been found in other extracellular subtilisin type serine proteases. The gene, hly, was expressed in another halophilic archaea, Haloferax volcanii, in a medium containing 18% salts by using a plasmid shuttle vector which has a novobiocin resistance determinant as a selectable marker.

Conjugate of N4-(4-carboxybutyryl)-ara-C and ethylenediamine-introduced dextran. Drug release profiles and further in vivo study of its antitumor effects.

In vitro and further in vivo work with a conjugate formed from the cytotoxic drug 1-beta-arabinofuranosylcytosine (ara-C) and dextran 2000 are described. In the preparation of this conjugate, functionalisation of ara-C was via N4-(4-carboxybutyryl)-ara-C (glu-ara-C), permitting conjugation with amino groups introduced by prior reaction of the oxidised dextran with ethylenediamine; by varying the proportions of the reaction components, 5.4 to 7.7% w/w loadings of ara-C were obtained. At physiological pH, in vitro, drug release from a 5.4% loaded conjugate was gradual and was dominantly ara-C; at lysosomal pH (pH 5) the release rate was much slower and more ara-U was formed. Antitumour effects were evaluated in L1210 leukaemic mice following single (1 day after inoculation) or double (2 and 6 days after inoculation) intraperitoneal injection of ara-C, glu-ara-C, or a 7.7% loaded conjugate at three dose levels. In all cases, the increase in lifespan was greatest following use of the conjugate, but the differences in the effects of ara-C and the conjugate were only significant at the lowest dose level. Glu-ara-C was virtually inactive under all conditions.

Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation.

The conformational change taking place in myoglobin concomitantly with the observed geometrical change at the heme-His(F8) linkage upon oxygenation is studied by normal mode analysis, which is based on the quadratic approximation of the conformational energy function. The heme-globin interaction energy increases for this change by 8.114 kcal/mol when both the heme group and the globin molecule are held rigid. When they are permitted flexibility, the interaction energy relaxes by 7.038 kcal/mol, and the difference (1.076 kcal/mol) is distributed as strain energy within the molecule. This increase is the work necessary for the heme group to move against the force exerted by the globin. If the force is assumed to be invariable during this move, the work is small, 0.276 kcal/mol, meaning that the force is strongly variable. Furthermore, this means that the heme group is located near the equilibrium point of the potential energy of the heme-globin interaction. The change in the localized strain energy stored in the force field at the linkage between the heme and the imidazole of HisF8 is estimated to be of the same order of magnitude as the distributed energy. The largest atomic displacements are observed at the region from the F helix to the beginning of the G helix, and secondary large displacements occur at several regions, i.e, the A helix, from the C helix to the CD corner, the E helix, and the C-terminal side of the H helix. All of these regions have strong dynamic interactions with the heme group, either directly or indirectly. Their secondary structures show complex deformations. In other parts, relatively rigid segments undergo rotational and/or bending changes in a way consistent with the large changes described above and close atomic packing within the molecule. The calculated conformational change is decomposed to vibrational normal modes of deoxymyoglobin. The magnitude of the conformational change, measured by the mass-weighted mean-square atomic displacement, is accounted for up to 92.0% by the 151 normal modes with frequencies lower than 40 cm-1. In descending order of contribution, the first six modes, each of which has a frequency lower than 12 cm-1, account for up to 57.4%. This means that the functionally important conformational change can well be expressed in terms of a relatively small number of collective low frequency normal modes.

Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction.

Dynamic properties of deoxymyoglobin are studied theoretically by the analysis of conformational fluctuations. Root-mean-square atomic fluctuations and distance fluctuations between different segments reveal the mechanical construction of the molecule. Eight alpha-helices behave as relatively rigid bodies and corner regions are more flexible, showing larger fluctuations. More particularly, corner regions EF and GH are specific in that flanking alpha-helices extend their rigidity up to a point in the corner region and the two rigid segments are connected flexibly at that point. The FG corner is exceptional. A segment from the F helix to the beginning of the G helix, in which the FG corner is included, becomes relatively rigid by means of strong interactions with the heme group. The whole myoglobin molecule is divided into two large units of motion, one extending from the B to the E helix, and the other from the F to the H helix. These two units are connected covalently by the EF corner. However, dynamic interactions between these two units take place mainly through contacts between helices B and G and not through the EF corner. From correlation coefficients between fluctuational motions of residues and the heme group, 55 residues are identified as having strong dynamic interactions with the heme moiety. Among them, 18 residues in the three segments, one consisting of residues from the C helix to the CD corner, a second consisting of the E helix, and a third from the F helix to the beginning of the G helix, are in close contact with the heme group. Twenty-two of the 55 residues are within four residues of the 18 residues in their sequential residue number and are more than 3 A away from the heme group. The other 15 residues are located further in the sequential residue number and are all found in helices A and H. They are more than 6 A away from the heme group. By the use of correlation coefficients of fluctuations between residues, it is found that dynamic interaction with the heme group is transmitted to the A helix and the beginning of the H helix in the direction Leu(E15)----[Val(All) and Trp(A12)]. The transmission to the C-terminal end of the H helix is mediated by a long segment, from the end of the EF corner to the beginning of the G helix, that lies on the heme group and has close contacts over a wide range.(ABSTRACT TRUNCATED AT 400 WORDS)

A halophilic extracellular protease from a halophilic archaebacterium strain 172 P1.

An unidentified halophilic archaebacterium strain 172 P1 produced three extracellular proteases in media containing 15-27% salts. One component, F-II, was purified to homogeneity. It is a serine protease that can be inhibited by phenylmethylsulfonyl fluoride and chymostatin. A high concentration of NaCl was required for its stability; in the presence of 25% NaCl, only 4% of the activity was lost by incubating at 60 degrees C for 30 min, while complete inactivation occurred in the presence of 5% NaCl. F-II is a thermophilic and halophilic protease. High activity was obtained at 75-80 degrees C when F-II was assayed in the presence of 25% NaCl. The optimal concentration of NaCl required was 10-14% when assayed at 70 degrees C with azocasein as substrate, though a halophilic characteristic was not distinct at lower temperatures. Hydrolyses of the synthetic substrates succinyl-alanyl-alanyl-prolyl-phenylalanyl-4-methylcoumaryl-7-amide or succinyl-alanyl-alanyl-alanyl-p-nitroanilide at 26 degrees C were maximal at 25 and 30% NaCl, respectively. F-II was most stable at pH 6-7, and its optimal pH was 10.7. Its molecular weight was estimated as 44,000-46,000 by sodium dodecyl sulfate--polyacrylamide gel electrophoresis and by gel filtration--high-pressure liquid chromatography. The sequence of the 35 N-terminal amino acid residues was determined and compared with that of other serine proteases.

A study on the quaternary structure change of hemoglobin in the ligation process.

In order to inquire into the molecular mechanism underlying the cooperative ligand binding to hemoglobin (Hb), conformational interaction at the interfaces between subunits are investigated on the basis of the atomic coordinates of human deoxy and human carbonmonoxy Hbs. Hypothetical intermediate structures are used, each of which is obtained from the procedure where one or more subunits in deoxy Hb are replaced by the corresponding CO-liganded subunits in carbonmonoxy Hb using the method of superimposition of two sets of atomic coordinates. When either alpha or beta subunit is substituted with the corresponding subunit in carbonmonoxy Hb, serious steric hindrances are produced between alpha 1FG4(92)Arg and beta 2C3(37)Trp or between alpha 1C6(41)Thr and beta 2FG4(97)His, all of which belong to the allosteric core affected directly by ligand binding. These steric hindrances become more serious when both alpha 1(alpha 2) and beta 2(beta 1) subunits are substituted. Therefore the change in the relative distance between iron atom and porphyrin by ligation results in strain in the C-terminal residues as an effect of the steric hindrance between the FG and C segments. However, no steric hindrance can be seen between subunits when the subunits in carbonmonoxy Hb are substituted with the corresponding subunits in deoxy Hb. The nature of the quaternary structural change from liganded to deoxy Hb seems to be different from that from deoxy to liganded Hb.