Three-dimensional structure of respiratory complex I from Escherichia coli in ice in the presence of nucleotides

Complex I (NADH:ubiquinone oxidoreductase) is the largest protein complex of bacterial and mitochondrial respiratory chains. The first three-dimensional structure of bacterial complex I in vitrified ice was determined by electron cryo-microscopy and single particle analysis. The structure of the Escherichia coli enzyme incubated with either NAD(+) (as a reference) or NADH was calculated to 35 and 39 A resolution, respectively. The X-ray structure of the peripheral arm of Thermus thermophilus complex I was docked into the reference EM structure. The model obtained indicates that Fe-S cluster N2 is close to the membrane domain interface, allowing for effective electron transfer to membrane-embedded quinone. At the current resolution, the structures in the presence of NAD(+) or NADH are similar. Additionally, side-view class averages were calculated for the negatively stained bovine enzyme. The structures of bovine complex I in the presence of either NAD(+) or NADH also appeared to be similar. These observations indicate that conformational changes upon reduction with NADH, suggested to occur by a range of studies, are smaller than had been thought previously. The model of the entire bacterial complex I could be built from the crystal structures of subcomplexes using the EM envelope described here.     

Water-borne seed transport and seed deposition during flooding in a small river-valley in Northern Germany

Water-borne seed transport and seed deposition during flooding were studied in the Upper Eider river (N-Germany) by direct sampling of the rivers seed content with aquatic seed traps and by analysing the number of deposited seeds on sedimentation mats which were exposed near the river on the soil surface during a flooding period of approx. three weeks.The number of seeds which were transported at the surface of the river Eider was continuously analysed by four aquatic seed traps for a period of 20 weeks (July–December 2000). To test the capture rate of these traps, a recapture experiment with colour marked seeds of Helianthus annuus L. was carried out. During the investigation period approx. 9000 seeds of 76 species were captured by the four aquatic seed traps. The number of trapped seeds varied both spatially (across the river profile) and temporally. Considering this variation and the capture rate of the traps, the water-borne seed transport was estimated to be 3139 seeds per week and meter of the river profile.The seed deposition during a flood in early spring 2002 was analysed by using 20 sedimentation mats. To distinguish effects of seed dispersal into patches from outside from seed rearrangement within patches, the water-borne seed transport was excluded from one half of the mats by fencing them with a woven fabric which was permeable for water but not for floating seeds. Outside of the exclosures 152 viable seeds of 26 species were deposited on the sedimentation mats while only one single seedling was found on mats from which water-borne seed transport was excluded.The results demonstrate that hydrochorous dispersal processes might play an important role in connecting otherwise fragmented populations in periodically flooded habitats along rivers.     

Self-Regulation Phenomena Applied to Bacterial Reaction Centers: 2. Nonequilibrium Adiabatic Potential: Dark and Light Conformations Revisited

Experimental and theoretical results in support of nonlinear dynamic behavior of photosynthetic reaction centers under light-activated conditions are presented. Different conditions of light adaptation allow for preparation of reaction centers in either of two different conformational states. These states were detected both by short actinic flashes and by the switching of the actinic illumination level between different stationary state values. In the second method, the equilibration kinetics of reaction centers isolated from Rhodobacter sphaeroides were shown to be inherently biphasic. The fast and slow equilibration kinetics are shown to correspond to electron transfer (charge separation) at a fixed structure and to combined electron-conformational transitions governed by the bounded diffusion along the potential surface, respectively. The primary donor recovery kinetics after an actinic flash revealed a pronounced dependence on the time interval (Δt) between cessation of a lengthy preillumination of a sample and the actinic flash. A pronounced slow relaxation component with a decay half time of more than 50 s was measured for Δt > 10 s. This component corresponds to charge recombination in reaction centers for which light-induced structural changes have not relaxed completely before the flash. The amplitude of this component depended on the conditions of the sample preparation, specifically on the type of detergent used in the preparation. The redox potential parameters as well as the structural diffusion constants were estimated for samples prepared in different ways.     

A Comparative Study on the Cleavage of Stereoisomeric Uridylyl (3',5')Uridines [D,D-, D,L- and L,D-UPU] by Acid,Base and Metal Ion Catalysts

Stereoisomeric uridylyl(3',5')uridines D,L-UpU andL,D-UpU were synthesised. Their cleavage was followed in thepresence of acid, base and metal ion catalysts to studywhether the stereochemistry affects the inherent reactivity ofthe internucleosidic phosphodiester bond, and whether the lowmolecular weight catalysts can distinguish between thesubstrates. The rate constants obtained were compared to thoseof D,D-UpU. The comparison shows that the stability of thephosphodiester bond does not depend on the stereochemistry ofthe sugar rings. In contrast slight reactivity differences areobserved in the presence of metal ion catalysts, whichsuggests that selective cleavage of stereoisomeric substrateseven by small molecular weight chemical catalysts may bepossible.     

Das Wachstum der Gewebskulturen in vitro und die Gurwitsch-Strahlung

Ohne Zusammenfassung     

Efficient tuning of potential parameters for liquid–solid interactions

Spherical and cylindrical water droplets on silicon surface are studied to tune the silicon–oxygen interaction. We use molecular dynamics simulations to estimate the contact angle of two different shaped droplets. We found that the cylindrical droplets are independent of the line tension as their three phases curvature is equal zero. Additionally, we compare an analytical model, taking into account or not the Tolman length and we show that for spherical small size droplets, this length is important to be included, in contrast to cylindrical droplets in which the influence of the Tolman length is negligible. We demonstrate that the usual convenient way to exclude linear tension in the general case can give wrong results. Here, we consider cylindrical droplets, since their contact angle does not depend on the droplet size in the range of few to 10ths of nanometres. The droplets are stabilised due to the periodic boundary conditions. This allows us to propose a new parameterisation for nanoscale droplets, which is independent the size of the droplets or its shape, minimising at the same time the calculation procedure. With the proposed methodology, we can extract the epsilon parameter of the interaction potential between a liquid and a solid from the nanoscaled molecular simulation with only as input the macrosized experimental wetting angle for a given temperature.     

New Structural Motifs for Hammerhead Ribozymes. Catalytic Activity of Abasic Nucleotide Substituted Ribozymes

Abstract

The synthesis of 1-deoxy-D-ribofuranose-3-(2-cyanoethyl N,N-diisopropylphosphoramidite) (6) from D-ribose and its incorporation into a hammerhead ribozyme is described.