Conformational investigation of alpha,beta-dehydropeptides. XVI. Beta-turn tendency in Ac-Pro-DeltaXaa-NHMe: crystallographic and theoretical studies.

The crystal structures of two diastereomeric alpha,beta-dehydrobutyrine peptides Ac-Pro-(Z)-DeltaAbu-NHMe (I) and Ac-Pro-(E)-DeltaAbu-NHMe (II) have been determined. Both dehydropeptides adopt betaI-turn conformation characterized by the pairs of (phi(i+1), psi(i+1)) and (phi(i+2), psi(i+2)) angles as -66, -19, -97, 11 degrees for I and -59, -27, -119, 29 degrees for II. In each peptide, the betaI turn is stabilized by (i + 3) --> i intramolecular hydrogen bonds with N...O distance of 3.12 A for I and 2.93 A for II. These structures have been compared to the crystal structures of homologous peptides Ac-Pro-DeltaVal-NHMe and Ac-Pro-DeltaAla-NHMe. Theoretical analyses by DFT/B3LYP/6-31 + G** method of conformers formed by these four peptides and by the saturated peptide Ac-Pro-Ala-NHMe revealed that peptides with a (Z) substituent at the C(beta) (i+2) atom of dehydroamino acid, i.e. Ac-Pro-DeltaVal-NHMe and Ac-Pro-(Z)-DeltaAbu-NHMe, predominantly form beta turns, both in vacuo and in polar environment. The tendency to adopt beta-turn conformation is much weaker for the peptides lacking the (Z) substituent, Ac-Pro-(E)-DeltaAbu-NHMe and Ac-Pro-DeltaAla-NHMe. The latter adopts a semi-extended or an extended conformation in every polar environment, including a weakly polar solvent. The saturated peptide Ac-Pro-Ala-NHMe in vacuo prefers a beta-turn conformation, but in polar environment the differences between various conformers are small. The role of pi-electron correlation and intramolecular hydrogen bonds interaction in stabilizing the hairpin structures are discussed.     

Optimized conditions for rapd analysis inPinus radiata

Summary Pinus radiata is the most important softwood plantation species in Australia and New Zealand. The improtance of this species in forestry has led to an increasing demand to improve the efficiency of selection time of the production population, which currently takes 13 yr by traditional methods. With the application of molecular biology techniques such as random amplified polymorphic DNA (RAPD) the selection period can be reduced to 6 yr. In this study, the conditions for RAPD were optimized and the feasibility of this marker system was investigated with different families ofPinus radiata from Tasmania and South Australia. Best concentrations of Taq-polymerase (1 U), magnesium chloride (2 mM), and template DNA (20 ng) were selected to test different polymerase chain reaction (PCR) thermocycler profiles. Devey's et al. (1996) program was the most effective for production of clear RAPD bands. Best conditions were investigated to screen 10–12 bp arbitrary Breasatec and Operon primers. Both types were found useful at detecting genetic variation between families. Seventy percent and thirty percent of the selected Bresatec and Operon primers, respectively, produced polymorphic bands.     

Environmental variables influencing the carbon balance at the alpine treeline: a modeling approach

Abstract. Growth of coniferous trees at alpine treeline locations has traditionally been viewed as primarily temperature dependent. In this study, we use a physiologically mechanistic process model, ATE-BGC (Alpine Treeline Ecotone - BioGeochemical Cycles), to study the effects of a suite of environmental variables on the carbon balance of krummholz growth forms of subalpine Abies lasiocarpa under environmental conditions representative of treeline locations in Glacier National Park, Montana, USA. We perform a sensitivity analysis of ATE-BGC to determine the relative effects of temperature, insolation, snow, rain, soil depth, leaf area index, winter injury and elevation on krummholz carbon balance. Our results indicate that ATE-BGC carbon balance estimates are most highly influenced by temperature and winter injury. Leaf area index, soil depth, rainfall, insolation and snowfall follow temperature and winter injury in their effect on carbon balance. Due to the sensitivity of the model to moisture related variables, we propose that local irregularities in the location of the alpine treeline ecotone are the result of localized xeric conditions.     

Effects of copper on periphyton communities assessed in situ using chemical-diffusing substrates

Chemical-diffusing substrates were designed to allow delivery of toxicants to mature periphyton communities under natural conditions without contaminating the surrounding environment. Artificial stream validation studies were conducted in which the effects of substrate-released copper (Cu) on periphyton communities were compared to those generated in a more conventional manner (via water column additions). Effects of copper on the following community parameters were assessed: total community biomass (measured as ash-free dry mass), relative chlorophyll a (chl a and adenosine triphosphate contents, and relative biomass of heterotrophic bacteria. Exposure of more laboratory periphyton communities to substrate-released Cu generated dose-response relationships and recovery models that were indistinguishable from those generated by the conventional route of exposure. The results of this study demonstrate the utility of chemical-diffusing substrates in field validations of laboratory toxicity tests and in investigations of the effects of stress history on periphyton tolerance to toxicants. This revised version was published online in September 2006 with corrections to the Cover Date.     

Different UmuC requirements for generation of different kinds of UV-induced mutations in Escherichia coli

An Escherichia coli strain bearing the dnaQ49 mutation, which results in a defective s subunit of DNA polymerase III, and carrying the lexA71 mutation, which causes derepression of the SOS regulon, is totally unable to maintain high-copy-number plasmids containing the umuDC operon. The strain is also unable to maintain the pAN4 plasmid containing a partial deletion of the umuD gene but retaining the wild-type umuC gene. These results suggest that a high cellular level of UmuC is exceptionally harmful to the defective DNA polymerase III of the dnaQ49 mutant. We have used this finding as a basis for selection of new plasmid umuC mutants. The properties of two such mutants, bearing the umuC61 or umuC95 mutation, are described in detail. In the umuC122:: Tn 5 strain harbouring the mutant plasmids, UV-induced mutagenesis is severely decreased compared to that observed with the parental umuDC ⁺ plasmid. Interestingly, while the frequency of UV-induced GC AT transitions is greatly reduced, the frequency of AT TA transversions is not affected. Both mutant plasmids bear frameshift mutations within the same run of seven A residues present in umuC ⁺; in umuC61 the run is shortened to six A whereas in umuC95 is lengthened to eight A. We have found in both umuC61 and umuC95 that translation is partially restored to the proper reading frame. We propose that under conditions of limiting amounts of UmuC, the protein preferentially facilitates processing of only some kinds of UV-induced lesions.     

Antibacterial activity of phosphono peptides based on 4-amino-4-phosphonobutyric acid

Abstract Phosphono dipeptides based on 4-amino-4-phosphonobutyric acid (phosphonic acid analogue of glutamic acid, GluP) were synthesized and evaluated for their antibacterial activity. Dipeptides containing N-terminal alanine, leucine, isoleucine, phenylalanine or lysine showed marked antibacterial activity against Escherichia coli , whilst those containing alanine, leucine, valine or proline were active against Serratia marcescens . AlaGluP and LeuGluP were nearly equipotent with the respective dipeptides based on 1-aminoethylphosphonic acid (phosphonic acid analogue of alanine). The structure-activity relationship, i.e. dependence of the activity of phosphono dipeptides on the nature of their N-terminal component, indicated that transport of the peptide through the bacterial cytoplasmic membrane constitutes a crucial step in its antibacterial activity.     

Identification of the cell surface and nuclear receptors for NGF in a breast carcinoma cell line

¹²⁵I-nerve growth factor (NGF) was found to be internalized and translocated to the nucleus of SKBr5 breast carcinoma cells. The cytoplasm and chromatin isolated from nonmitotic cells accumulated two-and five-fold, respectively, more of ¹²⁵I-NGF than the cells undergoing mitosis. MAb 20.4 developed against the NGF cell surface receptor immunoprecipitated the 80,000 M_r receptor from plasma membrane and two protein species from the chromatin; 90,000 M_r (major band) and 200,000 M_r (minor band). In SKBr5 cells, binding of NGF to the chromatin did not affect synthesis of rRNA. Proliferation of SKBr5 cells was slightly stimulated by NGF. In control melanoma A875 cells, which express the 230,000 M_r chromatin receptor, NGF inhibited both rRNA synthesis and cell proliferation. We suggest that the 90,000 M_r chromatin receptor expressed by SKBr5 cells represents a “nonactive”, ligand-binding subunit of the high molecular weight receptor for NGF. The critical role of the chromatin receptor for NGF in rRNA-dependent cell proliferation is discussed. © 1993 Wiley-Liss, Inc.     

A proposed framework for developing indicators of ecosystem health

Considerations involved in developing a suite of indicators to monitor regional environmental health, similar in conception to management use of leading economic indicators, are described. Linkages between human activities and well being and the state of the environment are considered essential to the evaluation of general environmental health. Biogeochemical and socioeconomic indicators are mutually affected by environmental degradation and examples of both categories of indicators are described. Desirable properties in indicators of environmental health vary with their specific management use. Different indicators are called for when collecting data to assess the adequacy of the environment, monitor trends over time, provide early warning of environmental degradation, or diagnose the cause of an existing problem. Tradeoffs between desirable characteristics, costs, and quality of information are inevitable when choosing indicators for management use. Decisions about what information to collect for which purpose can be made more rationally when available indicators are characterized and matched to management goals.     

Semiempirical calculations of the oxygen equilibrium isotope effect on binding of oxamate to lactate dehydrogenase

Semiempirical methods have been used in an attempt to predict theoretically the experimentally observed value of 0.9840 for the oxygen isotope effect on binding of oxamate to lactate dehydrogenase. The overall strategy involved vibrational analysis of oxamate in two different environments; that of the active site residues and in aqueous solution. The comparison of calculated values with the experimentally determined isotope effect proved the AM1 Hamiltonian to be superior to the PM3 Hamiltonian in this modelling. While most tested methods of accounting for solvent effects on the vibrational frequencies of the solute yielded similar results it turned out that what was crucial for the purpose of determination of the isotope effect was the model of oxamate in the active site of the enzyme. In particular, the major factor responsible for the inverse value of this isotope effect can be ascribed to the formation of an ordered, bifurcated hydrogen bond between the oxamate carboxylate and the guanidinium group of the active site histidine. Correspondence to: P. Paneth