Transition networks for modeling the kinetics of conformational change in macromolecules

The kinetics and thermodynamics of complex transitions in biomolecules can be modeled in terms of a network of transitions between the relevant conformational substates. Such a transition network, which overcomes the fundamental limitations of reaction-coordinate-based methods, can be constructed either based on the features of the energy landscape, or from molecular dynamics simulations. Energy-landscape-based networks are generated with the aid of automated path-optimization methods, and, using graph-theoretical adaptive methods, can now be constructed for large molecules such as proteins. Dynamics-based networks, also called Markov State Models, can be interpreted and adaptively improved using statistical concepts, such as the mean first passage time, reactive flux and sampling error analysis. This makes transition networks powerful tools for understanding large-scale conformational changes.     

Sensitive and selective viral DNA detection assay via microbead-based rolling circle amplification

We report a sensitive and efficient magnetic bead-based assay for viral DNA identification using isothermal amplification of a reporting probe.     

Biotinylated fluorescent peptide substrates for the sensitive and specific determination of cathepsin D activity.

Cathepsin D (CatD) is a member of the mammalian aspartic protease family and is involved in cellular protein degradation and in several pathological processes. A sensitive and specific assay for the determination of CatD activity in biological samples was developed. The peptide amide substrates Amca-EDKPILF downward arrowFRLGK(biotin)-CONH2 (I), Amca-EEKPIC(Acm)F downward arrowFRLGK(biotin)-CONH2 (II) and Amca-EEKPISF downward arrowFRLGK(biotin)-CONH2 (III) contain a CatD cleavage site (F downward arrowF) flanked by a N-terminal Amca-fluorophore (7-amino-4-methylcoumarin-3-acetic acid) and a C-terminal biotin moiety. Substrates II and III proved to be specific substrates containing only one cleavage site for CatD. After cleavage of the Phe-Phe bond by CatD all biotin conjugated peptides were removed with streptavidin-coated magnetic beads. The remaining fluorescent peptides in solution represent the amount of digested substrate. The versatility of this CatD digest and pull down assay was demonstrated by measuring the activity of CatD in different subcellular fractions of human EBV-transformed B cells and human monocytes. The described method based on the designed CatD substrates represents a valuable tool for routine assays.     

Factors Affecting Reproduction and Mortality Among Baboons in the Okavango Delta,Botswana

We present results of a 10-year study of free-ranging gray-footed chacma baboons (Papio ursinus griseipes) in the Okavango Delta of Botswana. The majority of deaths among adult females and juveniles were due to predation, while infants were more likely to die of infanticide. There were strong seasonal effects on birth and mortality, with the majority of conceptions occurring during the period of highest rainfall. Mortality due to predation and infanticide was highest during the 3-mo period when flooding was at its peak, when the group was more scattered and constrained to move along predictable routes. The reproductive parameters most likely to be associated with superior competitive ability—interbirth interval and infant growth rates—conferred a slight fitness advantage on high-ranking females. However, it was counterbalanced by the effects of infanticide and predation. Infanticide affected high- and low-ranking females more than middle-ranking females, while predation affected females of all ranks relatively equally. As a result, there were few rank-related differences in estimated female lifetime reproductive success.     

Characterization of microsatellite markers in sycamore (Acer pseudoplatanus L.)

Sycamore (Acer pseudoplatanus L.) is a tetraploid European hardwood tree species. The reproduction system of the insect‐pollinated trees and patterns of genetic variation are largely unknown. We isolated and characterized eight polymorphic microsatellite markers for Acer pseudoplatanus L. The high degree of polymorphism observed at these markers makes them useful to observe genetic variation patterns at various spatial scales and to analyse gene flow and the mating system. Primers developed for the amplification of microsatellites in A. pseudoplatanus were tested for 21 different species of genus Acer. Amplification products of the expected size were obtained in most cases.     

Host Location of a Pupal Parasitoid in a Tritrophic System Compared to a Model Offering Mechanosensory Cues Only

Several species of hymenopteran parasitoids are able to locate concealed pupal hosts by vibrational sounding. However, the specific role of this technique of mechanosensory host location has not yet been investigated in a natural, tritrophic system with multiple cues. Here we compared the host location of the pupal parasitoid Xanthopimpla stemmator in a tritrophic system with corn borer pupae in maize stem to the behavior on a paper model offering mechanosensory cues only. In general, the behavioral pattern and the behavioral states exhibited by host-searching female parasitoid were identical in the model and in the tritrophic system, while quantitative aspects differed. Our results demonstrate that vibrational sounding maintains its significance for host location in an environment with multiple cues, and that additional cues may increase responsiveness of females.     

Mutational Analysis of the Class IIa Bacteriocin Curvacin A and Its Orientation in Target Cell Membranes

To analyze the orientation in target cell membranes of the pediocin-like bacteriocin (antimicrobial peptide) curvacin A, 55 variants were generated by site-directed mutagenesis and their potencies against four different target cells determined. The result suggest that the somewhat hydrophilic short central helix (residues 19 to 24), along with the N-terminal β-sheet-like structure (residues 1 to 16), inserts in the interface region of the target cell membrane, with Ala22 close to the hydrophobic core of the membrane. The following hinge region, with Gly28 as an important residue, may then form a turn wherein Gly28 becomes positioned near the border between the interface and the hydrophobic regions, thus permitting the longer and more-hydrophobic C-terminal helix (residues 29 to 41) to insert into the hydrophobic core of the membrane. This helix contains three glycine residues (G33, G37, and G40) that form a putative helix-helix-interacting GxxxGxxG motif. The replacement of any of these glycines with a larger residue was very detrimental, suggesting their possible involvement in helix-helix interactions with a membrane-embedded receptor protein.     

Synthesis and reactivity of early-late heterobimetallic complexes displaying a η-tantalum-alkylidene to palladium interaction

Tantalaalkylidene compounds, CHR=TaCl₃L₂ (R=^tBu or CMe₂Ph, L=THF or 1/2dimethoxyethane) mixed with the cyclopalladated dimer [Pd(2-C₆H₄CH₂NMe₂)(μ-Cl)]₂, 1, afford good yields of heterodimetallic complexes [Pd(2-C₆H₄CH₂NMe₂)(μ-Cl)(μ-CHR=TaCl₃L], 3a, 3b, in which the Ta=C unit is η²-interacting with the palladium atom, while a chloride ligand is bridging the tantalum and the palladium atoms. These compounds are fairly stable in air in the solid state and also in solution at RT. The interaction of the Ta=C unit with Pd in these bimetallic compounds is weak as shown by the ready formation of [Pd(2-C₆H₄CH₂NMe₂)PyCl] and CHR=TaCl₃Py₂ upon treatement with pyridine. Compounds analogous to 3a, b can also be obtained with 12 electrons tantalum complexes. Thus treating the same cyclopalladated dimer 1 with CHR=Ta(OAr)₃ (OAr=2,6-diisopropylphenyloxy) led to a much more stable though electron deficient species: [Pd(2-C₆H₄CH₂NMe₂)(μ-Cl)(μ-CH^tBu=Ta(OAr)₃], 3c. Substitution in 3a of one chloride ion by an alkyl group occurred at the tantalum metal via reaction with ZnR₂ (R=---CH₂CMe₂Ph) leading to [Pd(2-C₆H₄CH₂NMe₂)(μ-Cl)(μ-CH^tBu=TaCl₃(CH₂CMe₂Ph)], 4 for which there is no free rotation around the new Ta---C bond and in which one of the methylene protons is strongly interacting with the palladium centre. This compound is believed to mimic an intermediate to the formation of tantalacarbyne derivative, which was obtained earlier via reaction of the uncomplexed tantalacarbene compound with dialkylzinc compounds.     

Distribution of conjugated linoleic acid and metabolites in different lipid fractions in the rat liver.

Conjugated linoleic acid (CLA) is known to provide certain health benefits in experimental animal models. The major CLA isomer in food is c 9,t11-CLA. A primary objective of this study was to investigate the uptake of c 9,t11-CLA and its downstream metabolites into various lipid fractions in the liver of rats fed either a high or low CLA diet (containing 0.1 or 0.8 g CLA/100 g diet, respectively). As expected, the levels of all conjugated diene (CD) fatty acids (CD 18:2 + CD 18:3 + CD 20:3 + CD 20:4) were elevated about 8-fold in the high CLA diet group. However, there was no change in the distribution of CLA and CLA metabolites into various lipid fractions due to CLA intake. Unlike linoleic acid or gamma-linolenic acid, which were distributed mainly in phospholipids, CD 18:2, CD 18:3, and CD 20:3 were incorporated primarily in neutral lipid. Furthermore, the incorporation of all nonconjugated unsaturated fatty acids was not perturbed by CLA. Regardless of the level of CLA in the diet, CD 20:4 was predominantly enriched in phosphatidylserine and phosphatidylinositol. In contrast, arachidonic acid was primarily enriched in phosphatidylcholine and less so in phosphatidylethanolamine. The above findings may have potential implication regarding the role of CLA in modulating eicosanoid metabolism.     

A general cloning strategy for divergent plant cytochrome P450 genes and its application in Lolium rigidum and Ocimum basilicum

The investigation of plant cytochrome P450 genes and enzymes is a field of growing interest. Apparently, an even greater diversity of cytochrome P450 genes exists in plants in comparison to other eukaryotes. This may be due to their role in the biosynthesis of secondary metabolites that are present in plants in an enormous variety. Most cloning approaches are hampered by the large sequence diversity of plant cytochrome P450 genes. We present a method to clone divergent cytochrome P450 ESTs by a nested RT-PCR-strategy. These ESTs were used for the subsequent cloning of the corresponding full-size cDNAs of divergent families via cDNA-library screening. Sixteen cytochrome P450 genes belonging to different cytochrome P450-families have been identified in this way, proving the efficacy of the strategy. Received: 1 December 2000 / Accepted: 26 February 2001