Conformation of P22 tailspike folding and aggregation intermediates probed by monoclonal antibodies.

The partitioning of partially folded polypeptide chains between correctly folded native states and off-pathway inclusion bodies is a critical reaction in biotechnology. Multimeric partially folded intermediates, representing early stages of the aggregation pathway for the P22 tailspike protein, have been trapped in the cold and isolated by nondenaturing polyacrylamide gel electrophoresis (PAGE) (speed MA, Wang DIC, King J. 1995. Protein Sci 4:900-908). Monoclonal antibodies against tailspike chains discriminate between folding intermediates and native states (Friguet B, Djavadi-Ohaniance L, King J, Goldberg ME. 1994. J Biol Chem 269:15945-15949). Here we describe a nondenaturing Western blot procedure to probe the conformation of productive folding intermediates and off-pathway aggregation intermediates. The aggregation intermediates displayed epitopes in common with productive folding intermediates but were not recognized by antibodies against native epitopes. The nonnative epitope on the folding and aggregation intermediates was located on the partially folded N-terminus, indicating that the N-terminus remained accessible and nonnative in the aggregated state. Antibodies against native epitopes blocked folding, but the monoclonal directed against the N-terminal epitope did not, indicating that the conformation of the N-terminus is not a key determinant of the productive folding and chain association pathway.     

Induction of autonomous endosperm in Lupinus luteus,Helleborus niger and Melandrium album by in vitro culture of unpollinated ovaries

Autonomous division of the endosperm was induced by in vitro culture of unpollinated ovaries or placenta-attached ovules in Helleborus niger, Lupinus luteus and Melandrium album. The induction frequencies for the three species were 50%, 10–20% and 0.1%, respectively. The endosperms contained up to 20 free nuclei; only a few ovules with 80–420 endosperm nuclei were found. Induction of autonomous division of the endosperm, which is unusual in amphimictic plants, was observed in three new species. No embryos appeared in the ovules. This suggests a developmental independence of the endosperm from the embryo in the culture of unpollinated ovaries or ovules.     

Effect of ligand binding and conformational changes in proteins on oxygen quenching and fluorescence depolarization of tryptophan residues

The rotational freedom of tryptophan residues in protein-ligand complexes was studied by measuring steady-state fluorescence anisotropies under conditions of oxygen quenching. There was a decrease in the oxygen bimolecular quenching constant upon complexation of trypsin and alpha-chymotrypsin with proteinaceous trypsin inhibitors, of lysozyme with N-acetylglucosamine (NAG) and di(N-acetyl-D-glucosamine) ((NAG)2) and of hexokinase with glucose. Binding of the bisubstrate analogue N-phosphonacetyl-L-aspartate (PALA) to aspartate transcarbamylase (ATCase) and binding of biotin to avidin resulted in increased oxygen quenching constants. The tryptophan of human serum albumin (HSA) in the F state was more accessible to oxygen quenching than that in the N state. With the exception of ATCase, the presence of subnanosecond motions of the tryptophan residues in all the proteins is suggested by the short apparent correlation times for fluorescence depolarization and by the low apparent anisotropies obtained by extrapolation to a lifetime of zero. Complex formation evidently resulted in more rigid structures in the case of trypsin, alpha-chymotrypsin and lysozyme. The effects of glucose binding on hexokinase were not significant. Binding of biotin to avidin resulted in a shorter correlation time for the tryptophan residues. The N --> F transition in HSA resulted in a more rigid environment for the tryptophan residue. Overall, these changes in the dynamics of the protein matrix and motional freedom of tryptophan residues due to complex formation and subsequent conformational changes are in the same direction as those observed by other techniques, especially hydrogen exchange. Significantly, the effects of complex formation on protein dynamics are variable. Among the limited number of cases we examined, the effects of complex formation were to increase, decrease or leave unchanged the apparent dynamics of the protein matrix.     

Wood anatomy ofTrimeniaceae

Four collections of three species ofTrimenia and one collection ofPiptocalyx were studied; early-formed and later-formed wood was analyzed for oneTrimenia. Liquid-preserved material permitted analysis of mucilage and starch storage in wood ofT. neocaledonica andP. moorei. BecausePiptocalyx is scandent whereasTrimenia is arborescent, wood differences relative to evolution of a climbing habit could be examined.Piptocalyx contrasts withTrimenia in having wider vessels, more numerous per mm², resulting in a conductive area five times greater per unit area than that of theTrimenia woods averaged.Piptocalyx has appreciably fewer bars per perforation plate and thus much greater conductive area per perforation plate than have the species ofTrimenia. Rays inPiptocalyx are much taller and wider than those ofTrimenia. Wood ofTrimeniaceae is highly primitive in its scalariform perforation plates, scalariform lateral wall pitting on vessels, relatively long vessels elements, and heterocellular rays. Imperforate tracheary elements are septate nucleate fibertracheids (or even libriform fibers) rather than tracheids, but loss of borders on pits (and thus lowered conductive function of the imperforate tracheary elements) can be explained by the development of these elements into starchstoring cells. Some fiber-tracheids inT. neocaledonica are enlarged mucilagecontaining cells. Details of vessel structure inTrimeniaceae are similar to those ofMonimiaceae (s. s.), but similarity to some other lauralean (annonalean) families may be found: in mucilage presence,Trimeniaceae resembleLauraceae rather thanMonimiaceae. Wood ofTrimeniaceae may be regarded as highly mesomorphic, corresponding to the moist habitats in which all of the species occur.     

A reassessment of the binding of napthaleneacetic acid by membrane preparations from maize

Naphthalene-1-acetic acid (NAA) binding by membrane fractions derived from maize has been re-evaluated. Using a computer curve-fitting procedure only one major type of NAA binding, in terms of binding affinity, could be identified. Auxins, antiauxins and structurally related compounds have been tested for their competitive effect on NAA binding and the inhibitor constants for a number of these have been determined. Extracts from various plant species have been examined for their NAA binding ability, but all showed much less binding than maize leaf or coleoptile preparations. The possibility of the NAA binding by maize extracts being due to a true hormone receptor is discussed.Abbreviations BA benzoic acid - CPIB p-chlorophenoxyisobutyric acid - 2,4-D 2,4-dichlorophenoxyacetic acid - DCB 2,4-dichlorobenzoic acid - IAA indolyl-3-acetic acid - NAA napthalene-1-acetic acid - 2-NAA napthalene-2-acetic acid - NAOA napthalene-2-oxyacetic acid - PA phenylacetic acid - PU phenylurea - 2,4,5-T 2,4,5-trichlorophenoxyacetic acid - TIBA 2,3,5-triiodobenzoic acid     

Incorporation of3H-thymidine into DNA and the activity of alkaline phosphatase in zinc-deficient fetal rat brains

The incorporation of³H-thymidine into DNA in the brains of the 17-day and 20-day old rat fetuses was significantly reduced by maternal zinc restriction during pregnancy. The activity of the enzyme thymidine kinase (EC 2.7.1.21) was similarly reduced in the zine-deprived fetal brains on days 14 and 20 of gestation, but not on day 17. Fetal brain alkaline phosphatase (EC 3.1.3.1) was significantly depressed by maternal zinc deprivation on days 17 and 20 of pregnancy. The data suggest an association between thymidine kinase and the reduced incorporation of³H-thymidine into DNA in the brains of 20-day old fetuses but not in animals on day 17. Alkaline phosphatase was however depressed at this stage. The suggestion is made that because of the complexity of brain development, future biochemical studies in this area should concern specific structures in the brain at particular critical stages during neurogenesis.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.