Modeling of protein loops by simulated annealing.

A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.     

Inferring landscape resistance to gene flow when genetic drift is spatially heterogeneous

In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the ‘true’ cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the ‘true’ costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the ‘true’ scenario (cost distance Mantel correlations), but this ‘true’ scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the ‘true’ scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data.     

Volume regulation by flounder red blood cells in anisotonic media

The nucleated high K, low Na red blood cells of the winter flounder demonstrated a volume regulatory response subsequent to osmotic swelling or shrinkage. During volume regulation the net water flow was secondary to net inorganic cation flux. Volume regulation the net water flow was secondary to net inorganic cation flux. Volume regulation after osmotic swelling is referred to as regulatory volume decrease (RVD) and was characterized by net K and water loss. Since the electrochemical gradient for K is directed out of the cell there is no need to invoke active processes to explain RVD. When osmotically shrunken, the flounder erythrocyte demonstrated a regulatory volume increase (RVI) back toward control cell volume. The water movements characteristic of RVI were a consequence of net cellular NaCl and KCl uptake with Na accounting for 75 percent of the increase in intracellular cation content. Since the Na electrochemical gradient is directed into the cell, net Na uptake was the result of Na flux via dissipative pathways. The addition of 10(-4)M ouabain to suspensions of flounder erythrocytes was without effect upon net water movements during volume regulation. The presence of ouabain did however lead to a decreased ration of intracellular K:Na. Analysis of net Na and K fluxes in the presence and absence of ouabain led to the conclusion that Na and K fluxes via both conservative and dissipative pathways are increased in response to osmotic swelling or shrinkage. In addition, the Na and K flux rate through both pump and leak pathways decreased in a parallel fashion as cell volume was regulated. Taken as a whole, the Na and K movements through the flounder erythrocyte membrane demonstrated a functional dependence during volume regulation.     

Transferrin, somatomedins and growth

Plasma transferrin is significantly positively correlated to the growth velocity in normal children and children with various growth disorders. In hypopituitary dwarfs, both plasma transferrin and somatomedin are significantly lower than in controls. Acute variations of the plasma transferrin levels could be involved in the regulation of the GH secretion by a feedback mechanism. Yet, transferrin is neither a somatomedin or a somatomedin-binding protein, and the mechanisms relating growth to transferrin remain unknown.     

Phylogenetic analysis of the pathogenic anaerobe Clostridium perfringens using the 16S rRNA nucleotide sequence.

Clostridium perfringens, the first pathogenic clostridium examined, was placed in the nonmycoplasma subgroup of the low-dG+dC-content gram-positive cluster on the basis of the results of a phylogenetic analysis in which we used 16S rRNA comparisons. The closest relative that has been identified to date is Clostridium pasteurianum.     

Seasonal coupling between phyto- and bacterioplankton in a sand pit lake (Créteil lake,France)

Phyto- and bacterioplankton biomass and activity were simultaneously measured during the course of one year in the shallow Créteil Lake (France).Phytoplankton was dominated, during the whole year, by small-sized organisms (10 to 25 µm). Bacteria were in a majority small coccoids (<0.3 µm). Phyto -and bacterioplankton abundances averaged respectively 3.3 × 10⁶ cells l^–1 and 6 × 10⁹ cells l^–1.The phasing of the activity and biomass periods suggest a close coupling between phyto- and bacterioplankton. There were two distinct periods of high activity and biomass. Maximal values were observed in summer but an early increase occurred also in winter. Low or undetectable phytoplankton excretion rates, when heterotrophic activity was maximum, indicated a bacterial uptake of up to 100% of the released algal products during the incubation period. Heterotrophic uptake measurements with both glucose and amino acids revealed a seasonal change of the substrates in the lake, glucose uptake being associated more with the maximum activity of the algae, while the amino acids uptake was relatively higher during their decline.The maximal photosynthetic rate averaged 21.5 mgC m^–3 h^–1 and mean Vmax values were 0.056 and 0.050 mgC m^–3 h^–1 respectively for glucose and amino acids uptake.     

Conformational study of native and acid-dissociated states of porcine lutropin (pLH) by vacuum circular dichroism and ultraviolet absorption spectroscopy

Porcine lutropin shares with ovine lutropin common structural features. They exhibit identical vacuum circular dichroism down to 170 nm with characteristic negative bands at 173, 194, and 210 nm. The band at 210 ± 1 nm is shifted to 201 nm upon dissociation with disappearance of the 194-nm band. For the two hormones the acid transition involves a significant loss of the three recognized periodic structures α helix, β sheet, and β turns of type II, unshields near the same number of tyrosyl residues (2.2 ± 0.7), and gives rise to an identical absorption difference at 287 nm in a two-step mechanism. However, pLH also exhibits noticeable differences: 5 to 10 times lower rates of acid transition with a lower pK_a (3.7 ± 0.1) and different transition behavior of tyrosine residues compared to ovine lutropin.     

Identification of N- and C-terminal corticotropin peptides in the Mr 80000 form of neurophysin

The 125I-labeled Mr 80000 form of neurophysin has been purified from bovine neurohypophysi. Tryptic digests of this species were analyzed, prior to or after treatment with carboxypeptidase B, by high-pressure liquid chromatography followed by isoelectric focusing and the fragments compared with those generated by a similar treatment of reference bovine 1-39 adrenocorticotropin. The ACTH peptides 22-39 and 1-8, as well as the 1-7 derivative of the latter were identified by those two independent criteria. This provides chemical evidence supporting the hypothesis [8] that high Mr neurophysin may contain the sequence of ACTH.     

Correlations between variations of electrical field at the body surface and contractions of the stomach in guinea pig.

1. The slow potentiel changes of the base line of the electrocardiogram recorded by cutaneous electrodes, here called EGEG (electrogastroenterogram) have been recorded simultaneously with the electromyogram and pressure variations of the stomach antrum. 2. Periodic fluctuations of EGEG, 400 microV amplitude, were correlated with activities of the antrum EMG consisting of 3 to 6 mV spikes superimposed on slow wave of depolarization, and with gastric intraluminal pressure of 5 to 7 cm of water. 3. An anticholinergic drug abolished all those activities. A gastric contracture flattened the EGEG. 4. Rhythmic distensions of the antrum induced a synchronous modulation of EGEG, the magnitude of which was correlated with the amplitude of distension. These result suggest that the origin of EGEG is essentially the movements of stomach.     

Association-dependent active folding of alpha and beta subunits of lutropin (luteinizing hormone).

The kinetics of the structural transition of ovine lutropin (luteinizing hormone) from a dissociated and partially unfolded state to a biologically active, folded and associated state were studied from pH 1.8 to 6.5 by difference spectroscopy, circular dichroism, light scattering and ultracentrifugation under various conditions of temperature and ionic strength. Between pH 2.8 and 5.3 there is a thermodynamically reversible equilibrium between the two states of the hormone with a half-transition pH of 4.3 ± 0.1 at 26 °C. The interconversion of native folding to dissociated state is strictly first-order, and most of the kinetic results can be described in terms of two exponential decays with lifetimes of 20 and 100 seconds at pH 2 and 26 °C with one intermediate. A second intermediate with a short lifetime (1.5 s) is detected with stopped-flow experiments; its spectroscopic contribution is small. Refolding from the dissociated state is always second-order in the concentration range studied (12 to 110 μm lutropin), with rates at 26 °C, 1.4 m⁻¹ s⁻¹ at pH 4.3 and 2.2 m⁻¹ s⁻¹ at pH 5.3. The temperature dependence of the rate constant of active folding at pH 5.3 corresponds to activation parameters $\text{ΔH}{}^1\text{= +23.5}\text{kcal mol}{}^{\mathrm{-1}}\text{and}\text{ΔS}{}^1\text{= +21.6}\text{cal deg}{}^{\mathrm{-1}}$ mol⁻¹.From these data and computer-simulation studies, a simplest possible mechanism is proposed that involves the formation of a loose complex between the α and β subunits of the hormone, followed by a slow step of formation of the active, folded state. In the pituitary gland this would be a necessary pathway towards the active form. The storage of the hormone in the gland would offer enough time for this activation step to proceed.