Structure of the two-subsite beta-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

The three-dimensional structure of the catalytically efficient β-xylosidase from Selenomonas ruminantium in complex with competitive inhibitor 1,3-bis[tris(hydroxymethyl)methylamino]propane (BTP) was determined by using X-ray crystallography (1.3 Å resolution). Most H bonds between inhibitor and protein occur within subsite −1, including one between the carboxyl group of E186 and an N group of BTP. The other N of BTP occupies subsite +1 near K99. E186 (pK_a 7.2) serves as catalytic acid. The pH (6-10) profile for is bell-shaped with pK_a’s 6.8 and 7.8 on the acidic limb assigned to E186 and inhibitor groups and 9.9 on the basic limb assigned to inhibitor. Mutation K99A eliminates pK_a 7.8, strongly suggesting that the BTP monocation binds to the dianionic enzyme D14⁻E186⁻. A sedimentation equilibrium experiment estimates a K_d ([dimer]²/[tetramer]) of 7 × 10⁻⁹ M. Similar k_cat and k_cat/K_m values were determined when the tetramer/dimer ratio changes from 0.0028 to 26 suggesting that dimers and tetramers are equally active forms.     

A glycosylated form of the human cardiac hormone pro B-type natriuretic peptide is an intrinsically unstructured monomeric protein

The N-terminal fragment of pro B-type natriuretic peptide (NT-proBNP) and proBNP are used as gold standard clinical markers of myocardial dysfunction such as cardiac hypertrophy and left ventricle heart failure. The actual circulating molecular forms of these peptides have been the subject of intense investigation particularly since these analytes are measured in clinical assays. Conflicting data has been reported and no firm consensus on the exact nature of the molecular species exists. Because these clinical assays are immunoassay-based, specific epitopes are detected. It is conceivable then that certain epitopes may be masked and therefore unavailable for antibody binding, thus the importance of determining the nature of the circulating molecular forms of these analytes. This situation is an unavoidable Achilles’ heel of immunoassays in general.A recombinant O-linked glycosylated form of proBNP has been show to mimic some of the properties of extracted plasma from a heart failure patient. In particular the recombinant and native material co-migrated as diffuse Western-immunostained bands on SDS-PAGE and each band collapsed to an apparent homogeneous band following deglycosylation. Thus, glycosylated-proBNP may be one such circulating form. Here we provide extensive physiochemical characterization for this O-linked protein and compare these results to other described circulating species, non-glycosylated-proBNP and NT-proBNP. It will be shown that glycosylation has no influence on the secondary and quaternary structure of proBNP. In fact, at moderate concentration in benign physiological neutral pH buffer, all three likely circulating species are essentially devoid of major secondary structure, i.e., are intrinsically unstructured proteins (IUPs). Furthermore, all three proteins exist as monomers in solution. These results may have important implications in the design of NT-proBNP/BNP immunoassays.     

Current perspectives in pulmonary surfactant — Inhibition, enhancement and evaluation

Pulmonary surfactant (PS) is a complicated mixture of approximately 90% lipids and 10% proteins. It plays an important role in maintaining normal respiratory mechanics by reducing alveolar surface tension to near-zero values. Supplementing exogenous surfactant to newborns suffering from respiratory distress syndrome (RDS), a leading cause of perinatal mortality, has completely altered neonatal care in industrialized countries. Surfactant therapy has also been applied to the acute respiratory distress syndrome (ARDS) but with only limited success. Biophysical studies suggest that surfactant inhibition is partially responsible for this unsatisfactory performance. This paper reviews the biophysical properties of functional and dysfunctional PS. The biophysical properties of PS are further limited to surface activity, i.e., properties related to highly dynamic and very low surface tensions. Three main perspectives are reviewed. (1) How does PS permit both rapid adsorption and the ability to reach very low surface tensions? (2) How is PS inactivated by different inhibitory substances and how can this inhibition be counteracted? A recent research focus of using water-soluble polymers as additives to enhance the surface activity of clinical PS and to overcome inhibition is extensively discussed. (3) Which in vivo, in situ, and in vitro methods are available for evaluating the surface activity of PS and what are their relative merits? A better understanding of the biophysical properties of functional and dysfunctional PS is important for the further development of surfactant therapy, especially for its potential application in ARDS.     

Interaction of human α-lactalbumin with fatty acids: Determination of binding parameters

The interaction of holo- and apo-forms of human alpha-lactalbumin with fatty acids was studied by a partition equilibrium method. Apo-alpha-lactalbumin, obtained by treatment with EDTA, displays one binding site for fatty acids, the association constants for oleic and palmitic acids being 1.9.10(6) and 4.2.10(5) M(-1), respectively. However, holo-alpha-lactalbumin was unable to bind fatty acids as measured by this technique. Likewise, no fatty acids bound to holo-alpha-lactalbumin, isolated using nondenaturing conditions, were detected by gas chromatography. These results demonstrate that the conformational change induced in alpha-lactalbumin by the removal of calcium enables the protein to interact with fatty acids.     

Processes involved in species saturation of ground‐dwelling ant communities (Hymenoptera,Formicidae)

The species saturation hypothesis in ground‐dwelling ant communities was tested, the relationship between local and regional species richness was studied and the possible processes involved in this relationship were evaluated in the present paper. To describe the relationship between local and regional species richness, the ground‐dwelling ant fauna of 10 forest remnants was sampled, using 10 1 m² quadrats in each remnant. The ants were extracted from the litter by using Winkler sacs. Using regression analyses, an asymptotic pattern between local and regional species richness was detected. This saturated pattern may be related to three processes: (i) high interspecific competition; (ii) habitat species specialization; or (iii) stochastic equilibrium. It is concluded that non‐interactive processes, such as stochastic equilibrium and habitat specialization may act as factors regulating species richness in this community. The predominance of locally restricted species, in all sampled remnants, seems to indicate the occurrence of a high degree of habitat specialization by the ant species. This result is evidence for the hypothesis that community saturation has been generated by non‐interactive processes. Although ants are frequently described as highly interactive, it is possible that interspecific competition is not important in the structuring of ground‐dwelling ant communities.     

一个造血模型的持久生存

考虑下述造血模型dN(t)/dt=-δN(t)-βθ^nN(t)/θ^n N^n(t) 2βθ^nN(t-τ）/θ^n N^n(t-τ)e^γτ,t≥0,其中δ、β、θ、γ、τ∈（0, ∞）,n∈（1, ∞）,得到持久生存的充分条件。     

Must There Be a Balance of Nature?

The balance of nature concept is an old idea that manifests itself in anumber of forms in population and community ecology. This paper focuseson population ecology, where controversy surrounding the balance ofnature takes the form of perennial debates over the significance ofdensity dependence, population regulation, and species interactions suchas competition. One of the most striking features of these debates, overthe course of the previous century in ecology, is the tendency to arguethe case on largely conceptual grounds. This paper explores twoquestions. Why this tendency to settle on conceptual grounds what is soobviously an empirical issue? Are there any good conceptual arguments tobe had in this area?     

Photogravitropic equilibrium in <Emphasis Type="Italic">Avena</Emphasis> coleoptiles: fluence rate–response relationships and dependence on dark adaptation and clinostating

Phototropism of Avena coleoptiles was measured in response to blue-light irradiation lasting between 2 and 24 h. During this time the coleoptiles established a bending angle of photogravitropic equilibrium that was dependent on the time of irradiation and also on the pretreatment in light or darkness prior to stimulation. The absolute threshold for the photogravitropic equilibrium in response to blue light was 10⁻⁸ μmol m⁻² s⁻¹. Photon fluence rate–response curves, which were generated after several hours of dark adaptation, had a characteristic shape with a prominent optimum in the middle of the dynamic range. Curves which were generated without prior dark adaptation displayed no such optimum. Clinostating dark-adapted coleoptiles caused an increase of sensitivity and responsiveness during a 2-h period of unilateral irradiation. The advantages and the drawbacks of long-term irradiation experiments for the investigation of phototropism and the generation of action spectra are discussed. Received: May 14, 2001 / Accepted: December 7, 2001     

Genetic structure of populations of the closely related species of Melanopsis (Gastropoda: Cerithiacea) in Israel

Population genetic structure in the species of Melanopsis were studied by means of cellulose acetate gel allozyme electrophoresis, on 26 Melanopsis populations from Israel: six of Melanopsis buccinoidea Olivier, 1801, eight of Melanopsis saulcyi Bourguignat, 1853, one of Melanopsis meiostoma Heller et Sivan, 2000 , 11 of Melanopsis costata Olivier, 1804, represented by two subspecies: M. costata costata Olivier, 1804 and M. costata jordanica Roth, 1839. 14 loci (nine polymorphic) were scorable: Aat, Alp, Est-1, Est-2, Gpi, Hbdh, Idh-1, Idh-2, Iddh, Mdh, Mdhp, Mpi, Pgdh, Pgm. Gametic disequilibrium was postulated. D-statistics was computed, indicating limited migration, not epistatic selection as the source of disequilibrium. Exact multilocus and multipopulation tests showed a statistically significant heterozygote deficit in 18 populations and seven polymorphic loci. Inbreeding, Wahlund's effect and codominant mode of selection were postulated as causing homozygote excess. Mantel test indicated a statistically significant association between the pairwise θ and geographic distance, and no association between Nm and the geographic distance. The mean gene flow estimates Nm, derived from either θ or private alleles technique, were consistent. Hierarchical F-statistics showed slight differences between the taxa. The process of speciation within the genus seems not yet completed.     

Application of the equilibrium concept to the development of agaric fruit-bodies, with special reference to their straight downward growth in light from below

Equilibrium, a concept of dynamics, is found to be applicable to the phototropic and gravitropic growth in agaric fruit-bodies. The fruit-bodies exposed to light from below grow straight downward without bending upward, and those exposed to light from obliquely below grow first downward and then upward by negative gravitropism. The fruit-bodies exposed to light from above grow upward. Fruit-bodies growing straight downward or upward do not change the direction of growth; they are in ‘equilibria’. The straight downward growth can be regarded as an ‘unstable equilibrium’ having a higher potential, and the straight upward growth as a ‘stable equilibrium’ having a lower potential. The change in the direction of growth can be explained by the change in the potential; the upward bending in fruit-bodies that have grown obliquely downward can be regarded as a ‘transition’ from the unstable equilibrium to the stable one.