Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.     

The convergent trajectories of bird communities along ecological successions in european forests

Summary There is much more variation in the composition of bird communities in the earlier open and semi-open seral stages of ecological successions in forested landscapes of Europe than later on in preforested and forested climactic stages. The demonstration of this trend is achieved from the study of four habitat gradients, two in the mediterranean region (Provence and Corsica) and two in central Europe (Burgundy, France and Poland). A multivariate analysis has been used to illustrate the dynamics of communities along these succession. Displays of the results in bivariate space as well as an illustration of the distributional profiles of some of the most characteristic species show that: i) there is a discrimination between the two mediterranean gradients and the two medioeuropean ones and ii) each succession starts with a very distinct set of species and then the four gradients regularly converge in the last climactic stage where there is almost no discrimination between communities. These results are discussed in the light of the history of European biotas during the Pleistocene. The reason why there is more variation in species composition in the earlier seral stages than in the later forested stages are discussed according to current theories on the role of habitat selection on speciation processes.     

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.     

A function describing all-sized trunk diameter distribution in warm-temperate rain forests

A simple relation (v-lnB) (u-lnx)=c was recognized betweenx as dbh (or individual basal area) andB as the cumulative basal area abovex, for various stands of warm-temperate rain forests of Yakushima Island, southern Japan (v, u andc, parameters). The model parameters explained a difference in the pattern of stand development between secondary succession after clear-felling and gap regeneration within primary forests.     

Purification and characterization of lymphocytic clonal growth factor (LCGF) derived from human-human hybridoma SH-76 cells

Human-human hybridoma SH-76 cells were found to produce a factor that supported the growth of lymphocytic cells at low densities. The factor was purified from serum-free conditioned medium of the hybridoma cells by a successive application of ammonium sulfate precipitation, DEAE-Toyopearl, TSK G3000 SW and DEAE-5PW column chromatograph. The purified factor was a 72K single protein. The factor showed marked growth stimulating effect on lymphocytic cell lines, but had no effect on the growth of human adhesive cancer cell lines. Thus, the factor is a lymphocytic clonal growth factor (LCGF), as found previously in human plasma (Miyata, 1988). The LCGF of SH-76 cells could be produced in growth factor-free RPMI medium and purified easily from the conditioned medium. The factor is inactivated by heating at over 80°C, but is much more stable than the LCGF in human plasma.     

Long-term vegetation change in the Juncus squarrosus grassland at Moor House,northern England

Data from the long-term experiment on sheep grazing versus zero sheep grazing (i.e. in an enclosure) on the composition of the Juncus squarrosus grassland at the Moor House NNR are presented. The data have been analysed to assess change in (1) the abundance of individual species, (2) higher plant and bryophyte communities, and (3) vegetation structure. The higher plant data suggested that both the enclosed-and grazed plots were changing in the same direction, but the enclosed plot was moving much faster. The general tendency was towards a blanket bog vegetation dominated by Eriophorum vaginatum and Calluna vulgaris. Juncus squarrosus has declined very quickly in the enclosed plot, but there has also been a slower decline in the grazed one. A significant increase in Calluna vulgaris has occurred only in the enclosed plot. In contrast, the bryophyte data showed completely different successional trajectories in the two treatment plots.The vegetation structure changed markedly after release from grazing, with a decrease in phytomass, but increase in necromass in the lowest height strata. There was no noticeable change in structure over the 18 year period in the grazed plot.Particular problems found in this study were that some species either fluctuated widely in response, or changed in a curvilinear manner.     

Tree species regeneration in a mid-elevation,temperate rain forest in Isla de Chiloé, Chile

The regeneration of canopy and subeanopy species in a mid-elevation, primary rain forest in the Coastal Range of Isla de Chiloé (42°30S), in the cold-temperate region of Chile, was studied by comparing seedling and sapling abundances under the forest canopy, and within 36 tree-fall gaps. The forest was dominated byAmomyrtus luma andLaurelia philippiana (33 and 32% of the main canopy individuals), and two subcanopy species (Myrceugenia ovata, andMyrceugenia planipes) were also important. Uncommon species in the canopy wereDrimys winteri, Amomyrtus meli, andRaphithamnus spinosus. Tree-fall gaps were created generally by the fall of several trees, and the main canopy species were the principal gap-makers. Gap sizes varied between 28 and 972 m², with a mean of 197 m². Seedling and sapling abundances indicate that the dominant species are capable of regenerating below the canopy, but they also germinate and show enhanced growth within small light gaps. For one of the common subcanopy species (M. planipes) and the two infrequent canopy species (D. winteri, andA. meli) regeneration seems to depend entirely on tree-fall gaps. Thus, in this forest, light gaps allow the persistence of infrequent canopy species, but seem less important for the regeneration and maintenance of dominant canopy species.     

Forest-level analysis of stability under exploitation: depensation responses and catastrophe theory

Stability analysis of whole forests is proposed as a qualitative tool for the study of forest responses to partial or patchy harvests or mortality. Instead of modeling every tree or stand, aggregate tree biomass is modeled. In order to aggregate stands, spatial effects must be incorporated. It is shown that depensation growth responses (reduced growth at low biomass) are common because forests often modify harch environments to be more suitable for their growth. Depensation can result from thinning, partial mortality, patchy cutting, or clearcutting, depending on forest type and abiotic factors. Examples of these types of behaviors are given. Stability analysis of different growth regimes under exploitation are related to catastrophe theory and to optimal harvesting policies. Such qualitative analysis is shown to be applicable to data-poor regions such as the tropics where there is great concern over responses of forests to exploitation.     

The effect of fluctuations in tidal inundation frequency on a salt-marsh vegetation

Over a period of 15 years recordings were made of the species cover in permanent plots on the salt marsh of one of the West Frisian Islands, Schiermonnikoog (The Netherlands). Correlations between annual changes in the cover of the major species, and fluctuations in the monthly frequency of inundation by seawater were studied. First, a spectral analysis was carried out on the inundation frequency data to look for predictable patterns. Subsequently, fluctuations were defined as deviations from these predictable patterns. In a repeated multiple regression model, the effects of the season in which the fluctuations occurred, and the elevational position of the plots on the salt marsh were studied as factors influencing the correlation patterns. The behaviour of various species is discussed in relation to their seed bank characteristics and their salt tolerance.     

Response to grazing after nine years of cattle exlusion in a Flooding Pampa grassland,Argentina

This paper reports on changes induced by the introduction of cattle in a grassland that had remained ungrazed for 9 yr, in comparison with two adjacent grasslands: one that remained enclosed and one that has been continuously subject to grazing. Basal cover was measured on 25 interception lines, each 1 m long, three times during one year. The variables studied were: total cover, cover of grasses and dicots, cover of creeping grasses, floristic composition, and dissimilarity among sites. At the first sampling, 2 yr after cattle re-introduction, the newly grazed site was more similar to the ungrazed than to the grazed site. The newly grazed site had very low cover of dicots; the species of dicots present were different from those found in the continuously grazed area. Creeping grasses had higher cover in the newly grazed site than in the other sites, and continued to increase. At the last sampling, one year later, the newly grazed site had become more similar to the contiuously grazed site. Only after 5 yr of cattle grazing the exotic dicots that were dominant in the continuously grazed site, were recorded in the re-opened site. The absence of propagules of these species or the absence of safe sites may account for this delayed invasion.