Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins

MALECON is a progressive combinatorial procedure for multiple alignments of protein structures. It searches a library of pairwise alignments for all three-protein alignments in which a specified number of residues is consistently aligned. These alignments are progressively expanded to include additional proteins and more spatially equivalent residues, subject to certain criteria. This action involves superimposing the aligned proteins by their hitherto equivalent residues and searching for additional Calpha atoms that lie close in space. The performance of MALECON is illustrated and compared with several extant multiple structure alignment methods by using as test the globin homologous superfamily, the OB and the Jellyrolls folds. MALECON gives better definitions of the common structural features in the structurally more diverse proteins of the OB and Jellyrolls folds, but it yields comparable results for the more similar globins. When no consistent multiple alignments can be derived for all members of a protein group, our procedure is still capable of automatically generating consistent alignments and common core definitions for subgroups of the members. This finding is illustrated for proteins of the OB fold and SH3 domains, believed to share common structural features, and should be very instrumental in homology modeling and investigations of protein evolution.     

DJ-1 Is a Redox-Dependent Molecular Chaperone That Inhibits α-Synuclein Aggregate Formation

Parkinson's disease (PD) pathology is characterized by the degeneration of midbrain dopamine neurons (DNs) ultimately leading to a progressive movement disorder in patients. The etiology of DN loss in sporadic PD is unknown, although it is hypothesized that aberrant protein aggregation and cellular oxidative stress may promote DN degeneration. Homozygous mutations in DJ-1 were recently described in two families with autosomal recessive inherited PD (Bonifati et al. 2003). In a companion article (Martinat et al. 2004), we show that mutations in DJ-1 alter the cellular response to oxidative stress and proteasomal inhibition. Here we show that DJ-1 functions as a redox-sensitive molecular chaperone that is activated in an oxidative cytoplasmic environment. We further demonstrate that DJ-1 chaperone activity in vivo extends to α-synuclein, a protein implicated in PD pathogenesis.     

Epidermal growth factor-mediated transient phosphorylation and membrane localization of myosin II-B are required for efficient chemotaxis

Epidermal growth factor (EGF) stimulation of prostate metastatic tumor cells results in transient phosphorylation and cellular localization of non-muscle myosin heavy chain II-B (NMHC II-B) with kinetics similar to those seen in chemotaxis. We demonstrate that expression of 18- and 72-kDa fragments derived from the NMHC II-B C terminus that contain EGF-dependent NMHC II-B phosphorylation sites serve as dominant-negative mutations for EGF-dependent NMHC II-B phosphorylation and localization. Both fragments inhibited the EGF-dependent phosphorylation by competing with NMHC II-B on the myosin heavy chain kinase. However, only expression of the 72-kDa fragment resulted in cells with abnormalities in cell shape, focal adhesions, and chemotaxis. We found that the 72-kDa (but not 18-kDa) fragment is capable of self-assembly. To our knowledge, these results provide the first strong evidence that EGF-dependent NMHC II-B phosphorylation is required for the cellular localization of NMHC II-B and that NMHC II-B is required for normal cell attachment and for chemotactic response.     

Detection and analysis of membrane interactions by a biomimetic colorimetric lipid/polydiacetylene assay

We describe applications of a colorimetric assay based on supramolecular assemblies of lipid-polydiacetylene vesicles for analysis and screening of membrane interactions of lipophilic enzymes, peptides, and ions and for study of the effects of lipid composition upon membrane properties. The lipid-polymer aggregates undergo visible and quantifiable blue-to-red transitions following interfacial interactions and perturbation by varied biochemical processes. Specifically, we show that the colorimetric assay can be tuned for selective detection of enzymes reacting with different lipid species. The experiments also demonstrate that the lipid/polymer platform facilitates screening of peptide-membrane interactions in multicomponent mixtures. The colorimetric vesicles can incorporate lipid species from different cellular sources facilitating analysis of the contribution of molecular components to membrane properties and lipid interactions.     

Speciation and the establishment of zonation in an intertidal barnacle: specific settlement vs. selection

The tropical barnacle Tetraclita forms a belt on hard substrates in the intertidal zone of the Red Sea. Based on morphological data, three distinct species were suggested to exist, occupying different vertical levels - T. barnesorum, T. rufotincta and T. achituvi. In this study we used molecular (12S mitochondrial ribosomal DNA) and ecological data to examine whether this morphological variability reflects genetic differences, or is a result of environmental factors. Adults and spats, collected from settlement plates, were censused and screened genotypically using single strand conformation polymorphism (SSCP) analysis, and settlement dynamics was recorded. We provide evidence for the existence of only two distinct species, and point out both phenotypic plasticity and convergence within and between the proposed species. Cyprids of T. achituvi settle specifically at the lower part of the Tetraclita belt, and feature one phenotype. In contrast, T. rufotincta, occupying the upper and middle portions of the Tetraclita belt, settles throughout the range, shows phenotypic plasticity (three variants), and presumably undergoes selection at the lower part. Thus, the vertical zonation of Tetraclita is produced by the combination of pre-settlement and post-settlement factors, in T. achituvi and T. rufotincta, respectively. The examined system may offer a model in which to study the mechanisms underlying sympatric speciation.     

Toward a PKB inhibitor: modification of a selective PKA inhibitor by rational design

Protein kinase B/Akt (PKB) is an anti-apoptotic protein kinase that has strongly elevated activity in human malignancies. We therefore initiated a program to develop PKB inhibitors, "Aktstatins". We screened about 500 compounds for PKB inhibitors, using a radioactive assay and an ELISA assay that we established for this purpose. These compounds were produced as combinatorial libraries, designed using the structure of the selective PKA inhibitor H-89 as a starting point. We have identified a successful lead compound, which inhibits PKB activity in vitro and in cells overexpressing active PKB. The new compound shows reversed selectivity to H-89: In contrast to H-89, which inhibits PKA 70 times better than PKB, the new compound, NL-71-101, inhibits PKB 2.4-fold better than PKA. The new compound, but not H-89, induces apoptosis in tumor cells in which PKB is amplified. We have identified structural features in NL-71-101 that are significant for the specificity and that can be used for future development and optimization of PKB inhibitors.     

Effects of the marine unicellular alga Nannochloropsis sp. to reduce the plasma and liver cholesterol levels in male rats fed on diets with cholesterol

The effects of Nannochloropsis were studied on rats consuming hypercholesterolemic diets. The whole biomass and the hexane/ethanol extract increased the plasma and hepatic eicosapentaenoic and docosahexaenoic acids levels, and reduced the cholesterol levels. We also observed a higher level of propionate, and a lower ratio between acetate and propionate. These data suggest the efficacy of Nannochloropsis in reducing cholesterol levels.     

Chickens fed with biomass of the red microalga Porphyridium sp. have reduced blood cholesterol level and modified fatty acid composition in egg yolk

The biomass of the red alga Porphyridium sp.constitutes a unique combination of soluble sulfatedpolysaccharide that accounts for about 70% of thealgal dry weight, and various polyunsaturatedfatty acids (PUFA) such as arachidonic andeicosapentaenoic acid (AA, 20:4 6 and EPA,20:5 3). In view of earlier results in ourlaboratory showing a reduction in serum cholesteroland triglyceride levels in rodents fed with red algalbiomass, we set out to examine the influence of algalbiomass as a feed additive on the metabolism ofchickens, with an emphasis on blood and eggcholesterol levels. For that purpose, lyophilizedalgal biomass was fed to 12–13, 30-week-old, WhiteLeghorn chickens for 10 days at a proportion of 5% or10% of the standard chicken diet. Twelve chickensfed with unsupplemented diet served as the control. No differences in body weight, egg number, and eggweight were found between the algal-fed chickens (atboth concentrations) and the control. However,chickens fed with algal biomass consumed 10% lessfood for both groups, and their serum cholesterollevels were significantly lower (by 11% and 28% forthe groups fed with 5% and 10% supplement,respectively) as compared with the respective valuesof the control group. Egg yolk of chickens fed withalgae tended to have reduced cholesterol levels (by10%) and increased linoleic acid and arachidonic acidlevels (by 29% and 24%, respectively). In addition,the color of the egg yolk was darker as a result ofthe higher carotenoid levels (2.4 fold higher) forchickens that fed with 5% supplement. Theseresults encourage the development of an improvedchicken feed having dietary fibers and polyunsaturatedfatty acids.     

Induction of antitumor immunity by indomethacin

Irradiated tumor cells given, together with indomethacin, to syngeneic mice induced an antitumor response and conferred protection against a challenge of a lethal dose of murine mammary (4T1) and lung (3LL) carcinoma cells. Continuous administration of indomethacin was crucial throughout the entire period of immunization and challenge, as no protection was achieved when the drug was given during only one of these procedures. Antitumor immunity was long-lasting and, when tested in the 4T1 model, 48% of mice were resistant to a second challenge of lethal tumor cells. Tumor-free immune mice that were given indomethacin for more than 300 days remained healthy with normal white blood cell counts and normal spleen size. Cells isolated from immune mice were able to kill tumor cells in culture after in vitro activation by interleukin-2, in a manner similar to cells from naive normal control mice. In addition, the mitogenic response of their T cells was as high as that of the control naive mice. While indomethacin was able to induce antitumor immunity to 4T1 and 3LL murine carcinoma cells, both of which contain a high concentration of endogenic prostaglandin E₂ (PGE2), no such immunity was achieved to murine tumor cells with a low concentration of endogenic PGE2. These results suggest a correlation between PGE2 concentration and the ability of indomethacin to induce antitumor immunity. We therefore suggest that an immunotherapy protocol with long-term dispensation of a tolerable dose of an immunomodulator, given together with irradiated autologous tumor cells, may stimulate antitumor responses to tumors containing high concentrations of endogenic PGE2. Received: 12 August 1999 / Accepted: 21 September 1999     

INTRASPECIFIC TRANSFER OF HERBICIDE RESISTANCE IN THE RED MICROALGA PORPHYRIDIUM SP. (RHODOPHYCEAE) VIA PROTOPLAST FUSION

Stable progeny doubly resistant to the herbicides sulfometuron methyl (SMM) and diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea] (DCMU) were obtained at a frequency of 2% on fusion of protoplasts derived from mutants of Porphyridium sp. (UTEX 637) that were resistant only to SMM (strain SMR) or DCMU (strain DC-2). In the presence of both herbicides, only the fusion progeny could grow; both parental mutants were inhibited. In the absence of SMM, the activity of acetohydroxy acid synthase (AHAS) in the wild-type strain was similar to that in DC-2, exceeding that of SMR by up to 4.5-fold. AHAS activities of all fusion progeny were lower than those of the wild-type strain and DC-2 but higher than that of SMR. In the presence of SMM, AHAS activities of all tested fusion progeny ranged between those of the two parental mutants. This result indicates that both types of AHAS, the type resistant to SMM and the sensitive type, originating from SMR and DC-2, respectively, were expressed in the fusion progeny. In the presence of DCMU, the photosynthetic activity of SMR was completely inhibited, whereas that of DC-2 was unaffected. The photosynthetic activity of the fusion progeny in the presence of DCMU was slightly lower than that of DC-2. Both the cell volume and the DNA content of the fusion progeny were similar to those of the parents. However, the genetic nature of the fusion products has not yet been elucidated. To the best of our knowledge, this is the first report on transfer of herbicide resistance via protoplast fusion in algae.