Cloning, purification, and characterization of galactomannan-degrading enzymes from Myceliophthora thermophila.

Genes of ß-mannosidase 97 kDa, GH family 2 (bMann9), ß-mannanase 48 kDa, GH family 5 (bMan2), and α-galactosidase 60 kDa, GH family 27 (aGal1) encoding galactomannan-degrading glycoside hydrolases of Myceliophthora thermophila C1 were successfully cloned, and the recombinant enzymes were purified to homogeneity and characterized. bMann9 displays only exo-mannosidase activity, the K(m) and k(cat) values are 0.4 mM and 15 sec(-1) for p-nitrophenyl-ß-D-mannopyranoside, and the optimal pH and temperature are 5.3 and 40°C, respectively. bMann2 is active towards galactomannans (GM) of various structures. The K(m) and k(cat) values are 1.3 mg/ml and 67 sec(-1) for GM carob, and the optimal pH and temperature are 5.2 and 69°C, respectively. aGal1 is active towards p-nitrophenyl-α-D-galactopyranoside (PNPG) as well as GM of various structures. The K(m) and k(cat) values are 0.08 mM and 35 sec(-1) for PNPG, and the optimal pH and temperature are 5.0 and 60°C, respectively.

Structure of the allosteric regulatory enzyme of purine biosynthesis.

Multi-wavelength anomalous diffraction (MAD) has been used to determine the structure of the regulatory enzyme of de novo synthesis of purine nucleotides, glutamine 5-phosphoribosyl-1-pyrophosphate (PRPP) amidotransferase, from Bacillus subtilis. This allosteric enzyme, a 200-kilodalton tetramer, is subject to end product regulation by purine nucleotides. The metalloenzyme from B. subtilis is a paradigm for the higher eukaryotic enzymes, which have been refractory to isolation in stable form. The two folding domains of the polypeptide are correlated with functional domains for glutamine binding and for transfer of ammonia to the substrate PRPP. Eight molecules of the feedback inhibitor adenosine monophosphate (AMP) are bound to the tetrameric enzyme in two types of binding sites: the PRPP catalytic site of each subunit and an unusual regulatory site that is immediately adjacent to each active site but is between subunits. An oxygen-sensitive [4Fe-4S] cluster in each subunit is proposed to regulate protein turnover in vivo and is distant from the catalytic site. Oxygen sensitivity of the cluster is diminished by AMP, which blocks a channel through the protein to the cluster. The structure is representative of both glutamine amidotransferases and phosphoribosyltransferases.

On the origin of bacterial resistance to penicillin: comparison of a beta-lactamase and a penicillin target.

Structural data are now available for comparing a penicillin target enzyme, the D-alanyl-D-alanine-peptidase from Streptomyces R61, with a penicillin-hydrolyzing enzyme, the beta-lactamase from Bacillus licheniformis 749/C. Although the two enzymes have distinct catalytic properties and lack relatedness in their overall amino acid sequences except near the active-site serine, the significant similarity found by x-ray crystallography in the spatial arrangement of the elements of secondary structure provides strong support for earlier hypotheses that beta-lactamases arose from penicillin-sensitive D-alanyl-D-alanine-peptidases involved in bacterial wall peptidoglycan metabolism.

Coaxial nickel/poly(p-phenylene vinylene) nanowires as luminescent building blocks manipulated magnetically.

A template-based strategy was developed which combines a wet-chemical technique and electrodeposition within nanoporous membranes. Morphological, structural and chemical characterization by means of electron microscopy and related techniques demonstrate unambiguously that coaxial nickel/poly(p-phenylene vinylene) (PPV) nanowires have been successfully synthesized. Moreover, modification of their optical and magnetic properties due to the nanoscale and the core-shell structure has been studied. The nickel-PPV nanowires exhibit a slightly blueshifted photoluminescence (PL), which is directly related to the tubular morphology of the PPV shell. The effect of the nickel core on the PL intensity of the PPV shell is discussed. The ferromagnetic behavior has been shown with the magnetization easy axis along the wire axis. These arrays of coaxial semiconducting polymer-metal nanowires embedded in a polymer membrane are interesting for flexible electronics and photovoltaic devices. Furthermore, their magnetic manipulation has been demonstrated, which opens the way to use them as multifunctional building blocks for bio-applications.

Elaboration of conjugated polymer nanowires and nanotubes for tunable photoluminescence properties.

Prototypal photoluminescent nanofibres of poly-(p-phenylene-vinylene) (PPV) were prepared by the wetting template method in polycarbonate nanoporous membranes with an easy all-in solution polymer precursor route. Both nanowires and nanotubes were obtained by varying the dilution of the polymer precursor in methanol prior to thermal conversion. PPV nanotubes exhibit unique features, such as blue-shifted emission at 2.80 eV, higher quantum yield, and longer fluorescence lifetime with respect to PPV films. These effects are attributed to the cancellation of interchain interactions that are consistent with nanoscale tubular structures formed from weakly interacting and short polymer chain segments. The synthesis of these objects opens up perspectives for tunable photoluminescence properties in the blue spectral range and for biochemical applications.

Steady state and transient photoluminescence in poly-p-phenylene vinylene films and nanofibers.

We report in this paper experimental data on steady state and transient photoluminescence of poly-p-phenylene vinylene in the form of nanofibers prepared with a template method and converted at 110 degrees C. Results are compared to those obtained from films of different thicknesses converted at the same temperature. Data are analyzed by a model of bimodal distribution of conjugation lengths and the photoluminescence band shapes, evaluated in the framework of this model, are also presented.

Dynamics of charge migration in poly(para-phenylene vinylene) films and nanocomposites with single walled carbon nanotubes.

We present in this paper a comprehensive study of the migration dynamics of the charges underlying transient photoluminescence (PL) processes in poly(para-phenylene vinylene) (PPV) samples from room temperature to 13 K. In order to interpret experimental data, we have modelled the long-time PL decays (from 100 to 1000 ps) using a time function proportional to [Formula: see text] in which the parameter α is evaluated in a Monte Carlo simulation on polymeric chains. The one dimensional chains (2000 sites long) are formed by random sequences of long and short conjugated segments whose bimodal distributions have been elaborated in previous works in order to reproduce the PL band shapes and peak positions. Intra-chain and inter-chain dynamics are taken into account in the migration of the photogenerated charges from short to long conjugated segments. The statistical analysis is performed by averaging over a total of 10(6) trials for each initial conditions. The values of α have been determined for pristine PPV films and PPV composite films with single-walled carbon nanotubes. This theoretical analysis is in good agreement with experimental data and provides a coherent description for the migration of the photogenerated charges in such inhomogeneous polymeric systems.

New trends in macromolecular X-ray crystallography.

Advances in experimental and computational techniques have reaffirmed the role of protein X-ray crystallography as one of the primary providers of structural information both to enhance our fundamental understanding of biological systems and also to assist the design and optimization of important therapeutics. Today, the most important challenge facing macromolecular X-ray crystallography is the need to grow suitable crystals of a given protein. Once this has been accomplished, most often the question is not whether the structure will be solved but rather how fast this will be done. A dramatic example of this is the crystal structure of cytochrome c oxidase. The search for crystallization conditions took about 15 years and then the structure was solved in about one year.

The refined three-dimensional structure of an insect virus at 2.8 A resolution.

The structure of the black beetle nodavirus has been refined at 2.8 A resolution by alternate use of restrained least-squares atomic coordinate refinement and phase refinement by real space averaging with the 5-fold non-crystallographic symmetry in the crystal. The coordinates were also refined by simulated annealing. The final R-factor for all data with I/sigma(I) > 4 was 22.1%. A total of 7692 atoms were refined in one icosahedral asymmetric unit which included 273 oxygen atoms of ordered water molecules. Three identical gene products of 407 amino acids form one icosahedral asymmetric unit. Each is located in a structurally unique position, identified as A, B or C, consistent with a T = 3 quasi equivalent lattice. Icosahedral pentamers are formed by A subunits while B and C subunits alternate about icosahedral 3-fold axes to form quasi hexamers. Five calcium ions are located within the icosahedral asymmetric unit and stabilize the quasi 3-fold related intersubunit contacts between A, B and C. The final model consists of coordinates for residues 56 to 379 of all three subunits and residues 20 to 31 from the C subunit only. Atom positions for the sugar-phosphate backbone were modeled for ten nucleotides close to the icosahedral 2-fold axes. Symmetry equivalent polyribonucleotides form a helical duplex at each icosahedral 2-fold axis. The three subunits display an eight-stranded beta-barrel fold, very similar to the subunit structures observed in most other icosahedral RNA viruses analyzed. Quasi equivalence is regulated by the ordered RNA and residues 20 to 31 in the C subunit to form a "flat inter subunit contact" at icosahedral 2-fold joints. The RNA and polypeptide are disordered at the quasi 2-fold joints and this results in a "bent inter subunit contact". Although similar quaternary structures were seen in T = 3 plant viruses studied, RNA did not play a role as a molecular switch in those structures. The autocatalytic, post assembly, cleavage of the initial gene product at residue Asn363/Ala364 to form a stable and infectious particle is probably the result of an acid catalyzed main-chain hydrolysis in which Asp75 is the proton donor. The reaction is initiated by assembly which places Asp75 in a hydrophobic environment created by quaternary interactions which raises its pK to 5.6. The region in which the reaction occurs is formed by an internal helical bundle that has not been seen in other virus structures.

Structural homology among four nodaviruses as deduced by sequencing and X-ray crystallography.

The genomic RNA2s of nodaviruses encode a single gene, that of protein alpha, the precursor of virion proteins beta and gamma. We compared the sequences of the RNA2s of the nodaviruses, black beetle virus (BBV), flock house virus, boolarra virus and nodamura virus, with the objective of identifying homologies in the primary and secondary structure of these RNAs and in the structure of their encoded protein. The sequences of the four RNAs were found to be similar, so that homologous regions relating to translation and RNA replication were readily identified. However, the overall, secondary structures in solution, deduced from calculations of optimal Watson-Crick base-pairing configurations, were very different for the four RNAs. We conclude that a particular, overall, secondary structure in solution within host cells is not required for virus viability. The partially refined X-ray structure of BBV (R = 26.4% for the current model) was used as a framework for comparing the structure of the encoded proteins of the four viruses. Mapping of the four protein sequences onto the BBV capsid showed many amino acid differences on the outer surface, indicating that the exteriors of the four virions are substantially different. Mapping in the beta-barrel region showed an intermediate level of differences, indicating that some freedom in choice of amino acid residues is possible there although the basic framework of the capsids is evidently conserved. Mapping onto the interior surface of the BBV capsid showed a high degree of conservation of amino acid residues, particularly near the protein cleavage site, implying that that region is nearly identical in all four virions and has an essential role in virion maturation, and also suggests that all four capsid interior surfaces have similar surfaces exposed to the viral RNA. Apart from a small portion of the C promoter, the amino terminus of the BBV protein (residues 1 to 60) is crystallographically disordered and the amino acid residues in that region are not well conserved. The disordered portion of the BBV protein clearly projects from the capsid inner surface into the interior of the virion, the region occupied by the viral RNA. In all four viruses, residues 1 to 60 had a high proportion of basic residues, suggesting a virus-specific interaction of the amino terminus with the virion RNA.

The crystal structure of human alpha-thrombin complexed with LY178550, a nonpeptidyl, active site-directed inhibitor.

The crystal structure of human alpha-thrombin in complex with LY178550, a nonpeptidyl, active site-directed inhibitor, has been solved to 2.07 A resolution by the method of X-ray crystallography. The final model of the complex has a crystallographic R-value of 21.5% (Rfree = 23.1%) with 0.014 A and 2.4 degrees standard deviation from ideal bond lengths and angles, respectively. Well-defined electron density was observed for the inhibitor in the active site. The inhibitor binds to the active site in an L-shaped manner, mimicking the bound conformation of the tripeptide arginal series of thrombin inhibitors (Chirgadze NY et al., 1992, American Crystallographic Association Meeting 20: 116 [Abstr. PB311]). The basic amidine of LY178550 forms a salt bridge with Asp 189 within the specificity pocket, while the 4-benzylpiperidine side chain engages in a number of hydrophobic interactions at the S2 and S3 binding sites. The inhibitor does not interact in any fashion with the active site sequence Ser 214-Gly 216, as occurs with many of the inhibitors studied previously. The indole N-H of the inhibitor forms a hydrogen bond to the gamma-oxygen of the catalytic serine (Ser 195).

High copy number integration into the ribosomal DNA of the yeast Phaffia rhodozyma.

This report describes a transformation system leading to stable high copy number integration into the ribosomal DNA (rDNA) of the astaxanthin-producing yeast Phaffia rhodozyma. A plasmid was constructed that contains the transposon Tn5 encoded kanamycin resistance gene (KmR) fused in frame to the 5'-terminal portion of the Phaffia actin gene. This marker, driven by the Phaffia actin promoter, confers resistance to G418 (Geneticin). The plasmid also contains a rDNA portion that comprises the 18S rDNA and promotes high copy integration leading to stable Phaffia transformants that maintained the plasmid at high copy number after 15 generations of non-selective growth. Phaffia, strain CBS 6938, was found to contain the rDNA units in clusters distributed over three chromosomes with a total copy number of 61. Phaffia transformants were shown to have over 50 copies of pGB-Ph9 integrated in tandem in chromosomes that contain rDNA loci. The chromosomal shifts that occur as a result of these integrations as shown by pulsed field electrophoresis strongly suggest that Phaffia is haploid.

Crystal structure study of Opsanus tau parvalbumin by multiwavelength anomalous diffraction.

The crystal structure of a small calcium-binding protein, the parvalbumin IIIf from Opsanus tau in which Tb was substituted for Ca, has been analysed by multiwavelength anomalous diffraction. Data at a resolution of 2.3 A were collected at three wavelengths near the L3 absorption edge of Tb (1.645-1.650 A), using the synchrotron radiation emitted by a storage ring and a multiwire proportional counter. The phases of the reflections were determined from this single derivative, without native data. Prior to any refinement, the resulting electron density map shows a good agreement with the model of the homologous carp parvalbumin in regions of identical amino-acid sequence.

Indole inhibitors of human nonpancreatic secretory phospholipase A2. 2. Indole-3-acetamides with additional functionality.

As reported in our previous paper, a series of indole-3-acetamides which possessed potency and selectivity as inhibitors of human nonpancreatic secretory phospholipase A2(hnps-PLA2) was developed. The design of these compounds was based on information derived from x-ray crystal structures determined for complexes between the enzyme and its inhibitors. We describe here the further implementation of this structure-based design strategy and continued SAR development to produce indole-3-acetamides with additional functionalities which provide increased interaction with important residues within the enzyme active site. These efforts led to inhibitors with substantially enhanced potency and selectivity.

Indole inhibitors of human nonpancreatic secretory phospholipase A2. 3. Indole-3-glyoxamides.

The preceding papers of this series detail the development of functionalized indole-3-acetamides as inhibitors of hnps-PLA2. We describe here the extension of the structure-activity relationship to include a series of indole-3-glyoxamide derivatives. Functionalized indole-3-glyoxamides with an acidic substituent appended to the 4- or 5-position of the indole ring were prepared and tested as inhibitors of hnps-PLA2. It was found that the indole-3-glyoxamides with a 4-oxyacetic acid substituent had optimal inhibitory activity. These inhibitors exhibited an improvement in potency over the best of the indole-3-acetamides, and LY315920 (6m) was selected for evaluation clinically as an hnps-PLA2 inhibitor.

Indole inhibitors of human nonpancreatic secretory phospholipase A2. 1. Indole-3-acetamides.

Phospholipases (PLAs) produce rate-limiting precursors in the biosynthesis of various types of biologically active lipids involved in inflammatory processes. Increased levels of human nonpancreatic secretory phospholipase A2 (hnps-PLA2) have been detected in several pathological conditions. An inhibitor of this enzyme could have therapeutic utility. A broad screening program was carried out to identify chemical structures which could inhibit hnps-PLA2. One of the lead compounds generated by the screening program was 5-methoxy-2-methyl-1-(phenylmethyl)-1H-indole-3-acetic acid (13a). We describe the syntheses, structure--activity relationships, and pharmacological activities of a series of indole-3-acetamides and related compounds derived from this lead. This SAR was undertaken with the aid of X-ray crystal structures of complexes between the inhibitors and hnps-PLA2 which were of great value in directing the SAR.

Integrated bioproduction and extraction of 3-methylcatechol.

Pseudomonas putida MC2 is a solvent-tolerant strain that accumulates 3-methylcatechol. In aqueous media, 10 mM of 3-methylcatechol was produced and production was limited by 3-methylcatechol toxicity to the biocatalyst. Production levels increased by introduction of a second, organic phase that provides the substrate toluene and extracts the product from the culture medium. Octanol was shown to be an appropriate second phase with respect to tolerance of the strain for this solvent and with respect to partitioning of both substrate and product. Per unit of overall reactor volume (octanol and water), best results were obtained with 50% (v/v) of octanol: an overall 3-methylcatechol concentration of 25 mM was reached with 96% of the product present in the octanol phase. These product concentrations are much higher than in aqueous media without organic solvent, indicating that biocatalysis in an organic/aqueous two-phase system is an improved set-up for high production levels of 3-methylcatechol.

Characterization of a GH family 3 ß-glycoside hydrolase from Chrysosporium lucknowense and its application to the hydrolysis of ß-glucan and xylan.

The Bxl5-gene encoding a GH3 glycoside hydrolase of Chrysosporium lucknowense C1 was successfully cloned, the homologous recombinant product was secreted, purified and characterized. Bxl5 (120 ± 5 kDa) was able to hydrolyze low molecular weight substrates and polysaccharides containing ß-glucosidic as well as ß-xylosidic residues. The K(m) and V(max)/E values were found to be 0.3mM and 88 s(-1) on p-nitrophenyl-ß-d-glucopyranoside (PNPG), and 13.5mM and 1.8s(-1) on p-nitrophenyl-ß-d-xylopyranoside (PNPX). Optimal pH and temperature for Bxl5 were 4.6 and 75°C for the PNPG hydrolysis, and 5.0-5.5 and 70°C for PNPX hydrolysis. The enzyme was quite stable when incubated at elevated temperatures up to 65°C. Bxl5 hydrolyzes polymeric ß-glucans by the exo-mechanism allowing their complete conversion to d-glucose and is effective for xylan hydrolysis in combination with endo-acting xylan-degrading enzymes. The enzyme seems to be a very promising for bioconversion purposes.

Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield.

Pseudomonas putida KT2440-JD1 was derived from P. putida KT2440 after N-methyl-N'-nitro-N-nitrosoguanidine (NTG)-mutagenesis and exposure to 3-fluorobenzoate (3-FB). The mutant was no longer able to grow using benzoate as a sole carbon source, but co-metabolized benzoate to cis, cis-muconate during growth on glucose, which accumulated in the growth medium. The specific production rate (q(pm)) was 0.18±0.03 g cis, cis-muconate/(g(DCW) h) in continuous cultures, and increased to 1.4 g cis, cis-muconate/(g(DCW) h) during wash-out cultivation. Transcriptome analysis showed that the cat operon was not induced in P. putida KT2440-JD1 in the presence of 5mM benzoate, due to a point mutation in the highly conserved DNA binding domain of the transcriptional regulator (catR) of the cat operon. The ben operon was highly expressed in the presence of benzoate in the mutant and its parental strain. This operon contains PP_3166 (catA2), which was shown to be a second catechol 1,2-dioxygenase besides catA. P. putida KT2440-JD1 is the first cis, cis-muconate-accumulating mutant that was characterized at the genetic level. The specific production rate achieved is at least eight times higher than those reported for other cis, cis-muconate-producing strains.

Chrysosporium lucknowense arabinohydrolases effectively degrade sugar beet arabinan.

The filamentous fungus Chrysosporium lucknowense (C1) is a rich source of cell wall degrading enzymes. In the present paper four arabinose releasing enzymes from C1 were characterized, among them one endoarabinanase, two arabinofuranosidases and one exoarabinanase. Combinations of these enzymes released up to 80% of the arabinose present in sugar beet arabinan to fermentable monosugars. Besides the main product arabinobiose, unknown arabinose oligomers are produced from highly branched arabinan when endoarabinanase was combined with exoarabinanase and/or arabinofuranosidase. All described arabinose releasing enzymes are temperature stable up to 50 degrees C and have a broad pH stability. This makes C1 arabinohydrolases suitable for many biotechnical applications, like co-fermentation bioethanol production.