Molecular dynamics simulations of phenylimidazole inhibitor complexes of cytochrome P450 cam

Molecular dynamics simulations have been performed on three phenylimidazole inhibitor complexes ofP450 _cam, utilizing the X-ray structures and the AMBER suite of programs. Compared to their corresponding optimized X-ray structures, very similar features were observed for the 1-phenylimidazole (1-PI) and 2-phenylimidazole (2-PI) complexes during a 100 ps MD simulation. The 1-PI inhibitor binds as a Type II complex with the imidazole nitrogen as a ligand of the heme iron. Analysis of the inhibitor-enzyme interctions during the MD simulations reveals that electrostatic interactions of the imidazole with the heme and van der Waals interactions of the phenyl ring with nearby hydrophobic residues are dominant. By contrast, 2-PI binds as a Type I inhibitor in the substrate binding pocket, but not as a ligand of the iron. The interactions of this inhibitor are qualitatively different from that of the Type II 1-PI, being mainly electrostatic/H-bonding interactions with a bound water and polar residues. Although the third compound, 4-PI, in common with 1-PI, also binds as a Type II inhibitor, with one nitrogen of the imidazole as a ligand to the iron, the MD average binding orientation deviates significantly from the X-ray structure. The most important changes observed include: (1) the rotation of the imidazole ring of this inhibitor by about 90° to enhance electrostatic interactions of the imidazole NH group with the carbonyl group of LEU244, and (2) the rotation of the carbonyl group of ASP251 to form a H-bond with VAL254. An analysis of the H-bonding network surrounding this substrate in the optimized crystal structure revealed that there is no H-bonding partner either for the free polar NH group in the imidazole ring of 4-phenylimidazole or for the polar carbonyl group of the nearby ASP251 residue. The deviation of the dynamically averaged inhibitor-enzyme structure of the 4-PI complex from the optimized crystal structure can therefore be rationalized as a consequence of the optimization of the electrostatic interactions among the polar groups.     

Shoot regeneration after fire or freezing temperatures and its relation to plant life-form for some heathland species

Shoot regeneration after prescribed burning or following the freezing temperatures of winter was monitored for nineteen heathland species present in an Arctostaphyleto-Callunetum community in northeast Scotland. Species whose renewal buds were near the surface of the ground started to grow earlier in the spring than species with renewal buds above the surface, but grouping species according to the position of their renewal bud (i.e. their life-form) did not account for all of the interspecific variation apparent. In the case of shoot regeneration after fire, species whose renewal buds were destroyed by fire because they were above-ground started to regenerate about the same time as species with belowground buds, protected from fire, but reached their maximum frequency of occurrence later. Grouping species by life-form was of limited value as a means of interpreting this interspecific variation in the timing of shoot regeneration after fire. It would be unwise to use plant life-form as the sole basis for interpreting or predicting a species' response to temperature stress when extreme temperatures occur regularly, as they do in heathland. The possible use of other plant traits to interpret and predict interspecific variation in the regeneration rate of heathland plants is discussed.Nomenclature follows Tutin et al. (1964–1980) for vascular plants. Acknowledgements. The Nature Conservancy Council and Mr J. J. Humphries kindly allowed Dinnet Moor to be used for the work presented here. One of us (RJR) received financial support for field work from the Natural Sciences and Engineering Research Council of Canada.     

Organization and dynamics of lipids in bovine brain coated and uncoated vesicles

Three characteristics have been demonstrated by the chemical analysis of bovine brain coated vesicles following removal of the coat proteins: a high protein content, a high cholesterol/lipid ratio and a high percentage of phosphatidylethanolamine amongst the phospholipids.The study of lipid bilayer organization and dynamics has been performed using the fluorescent probes pyrene and parinaric acid (cis and trans). This has allowed the study of both lateral mobility and rotational motion in the lipid bilayer of the coated and uncoated vesicles.Lateral mobility in the fluid phase of the lipid is slightly reduced by the presence of the clathrin coat, as indicated by the lower diffusion coefficient of pyrene in coated compared with uncoated vesicles.At all temperatures from 6° to 30°C, solid-phase domains, probed by trans parinaric acid, coexist with fluid-phase domains in the lipid bilayer. The temperature dependence of the parinaric acid lifetimes and of their amplitudes strongly suggests that the solid phase domains decrease in size with temperature, both in coated and uncoated vesicles.However, the difference in the value of the anisotropy at long times (r ), between coated and uncoated vesicles (a difference which is more pronounced for cis than for trans parinaric acid), indicates that the presence of the clathrin coat introduces disorder in the surrounding lipids, thus suggesting a possible role of the clathrin in the formation of the pits on the plasma membrane.Abbreviations CVs coated vesicles - UVs uncoated vesicles - TLC thin layer chromatography - DMSO dimethylsulfoxide - DPPC dipalmitoylphosphatidylcholine - cis Pna cis parinaric acid - (9,11,13,15-cis-trans-trans-cis) octadecatetraenoic acid - Trans Pna Trans parinaric acid - (9,11,13,15-all-trans) octadecatetraenoic acid     

Mutant hemoglobin stability depends upon location and nature of single point mutation

The temperature dependence of the rates of heme release from the beta subunits of methemoglobin A and 5 beta mutant methemoglobins has been determined. The rates were largest for two hemoglobins with mutations distal to heme, previously known to be unstable. The other 3 mutants also released heme faster than A. These hemoglobins, with single point mutations at the alpha 1/beta 2 interface, were previously thought to be stable. The low reported yields of the 5 mutant proteins covaries with the relative rates of heme release from the met species.     

Evolutionary stable strategies and game dynamics for n-person games

This note contains a generalization of the definition of an evolutionary stable strategy and of the corresponding game dynamics from 2-person to n-person games. This broader framework also allows modelling of several interacting populations or of populations containing different types of individuals, for example males and females.     

Species turnover in deciduous forest vegetation

Summary Permanent quadrats were marked out in two areas of hardwood forest vegetation in 1969, and listings of their vascular plant species were taken on several occasions over the snow-free seasons of 1969, 1970, 1971 and 1976. Over the period of study, mean numbers of species per m² remained virtually constant, but variations in the species compositions of individual quadrats were such that mean turnover ratios of 0.115 and 0.085, respectively, were computed for the two stands. Between 1969 and 1976 averages of 20% and 14%, respectively, of the species found in individual quadrats were replaced. This was not accomplished by qualitative changes in the floras of the two stands. Rather, it reflects the operation of a system of continuous rearrangements of species in the small quadrats of both sample areas.Taxonomical nomenclature and life-form system used in this study are according to Gleason & Cronquist (1963).William Phillips, Ian Sutherland and Sheila Thompson helped in the field; Professor Keith Wade commented on the material; Abal Sen drafted the diagram; and the research is part of that funded by the National Research Council of Canada.     

Änderungen in der Stickstoffversorgung auf Dauerflächen im Brachland

Summary Starting in 1968 plant succession and nitrogen status in the top soil of an old field was investigated. The soil is a calcareous loam which was sterilized by heating. In the absence of human influence distinct successional stages with characteristic floristical and physiognomical features were observed. During the first six years vegetational development was characterized by competition between therophytes and hemicryptophytes. Agricultural treatments such as annual ploughing (spring, summer) and cutting (autumn) were found to change the trend of the succession.Five years after starting the experiment total nitrogen content in the top soil of the control area had increased slightly, while the ploughed plots persisted in their low values. A comparison of the nitrogen mineralisation between 1970 and 1974 showed decreasing amounts of mineral nitrogen in the later stage (1970: 67 kg N_min/ha/30 weeks; 33 kg N_min/ha/30 weeks). On the other hand, mineral nitrogen supply on the ploughed plots was not significantly different after the five-years-period. It is suggested that in old-field vegetation the external nitrogen cycle of the early therophyte stage changed to an internal one when long-lived hemicryptophytes, rhizome- and root-budding geophytes became dominant.Tables 1 to 4 show the vegetation development under different treatments; the figures represent average cover values per vegetation season using Londo's (1975) scale. Table 5 contains the total nitrogen concentration values in the uppermost of 10 cm of mineral soil, and Table 6 lists the values for soil volume, mean soil temperatures, average water content, and mineral nitrogen supplies for 1970 and 1974.

Contribution to the Symposium of the Working Group for Succession Research on Permanent Plots, held at Yerseke, the Netherlands, October 1975.     

Dynamics of benthic algal vegetation and environment in Dutch estuarine salt marshes studied by means of permanent quadrats

Summary Knowledge of the spatial structure of benthic algal vegetations in salt marshes, consisting of about 100 species of blue-green, green, brown and red algae, formed the basis of a detailed study into the dynamics of the algal mat.The temporal changes in algal vegetations and concomitant processes in their environment were studied in 27 permanent quadrats (PQs), plotted in tidal salt marshes and along brackish inland waters in the SW Netherlands. Once a month vegetation and environment of the PQs were examined over the period March 1968-February 1971. From the Spearman rank-correlation between vegetational and environmental parameters it appeared that in semiterrestrial and terrestrial environments the average number of algal species in a relevé and the average similarity between the species composition of successive relevés obtained from one PQ have a significant positive correlation with the stability of the substrate, and hardly any correlation with fluetuations in soil-moisture content and salinity of the soil moisture and with the maximum cover percentage of the phanerogams.Stable substrates tend to bear stable algal mats, as appeared from quantitative data. Small and moderate fluctuations in soil-moisture content and salinity of the soil moisture have no limiting influence on the algal cover degree. During periods of extremely high salinity and concomitant extremely low soil-moisture contents that coincide with evaporation surpluses, the green algal mat bleaches and decreases in cover in semi-terrestrial and terrestrial environments. Below 20% the soil-moisture content is limiting for the expansion of a mat of green algae (Rhizoclonium riparium, Percursaria percursa, Enteromorpha torta, E. prolifera) and Vaucheria species. The mat desiceates and bleaches but recovers after increase of the soil-moisture content above 20% within one month. Two weeks of severe frost (temperature down to – 10°C) do not influence the cover degree of the algal mat in aquatic branckish PQs, but the cover degree in semi-terrestrial PQs decreases. Short lasting soil-moisture salinities of 130–190 Cl^– have no limiting effect on the expansion of the algal mat.Nomenclature authorities are given in Table 3.Contribution to the Symposium of the Working Group for Succession Research on Permanent Plots, held at Yerseke, The Netherlands, October 1975.Communication No. 163 of the Delta Institute for Hydrobiological Research, Yerseke.     

The population ecology of gammarus tigrinus (sexton) in the reed beds of the Tjeukemeer

The population ecology of Gammarus tigrinus (Sexton) was studied in the Tjeukemeer during 1969 and 1970. G. tigrinus reaches very high densities — up to 24,000/m² in parts of the study area. In 1970, the summer densities were 2–21/2 times greater than in 1969. Individuals do not grow to such large sizes in the summer as at other times of the year. Females begin to carry eggs in March or April and reproduction ceases in November. Large females have larger broods than smaller animals and the average size of the brood varies with the time of year. The egg incubation period and growth rate are dependent upon temperature. At summer temperatures females became sexually mature after about four weeks and the egg incubation period is about io days. The entire population is turned over about three times during the year. A combination of rapid growth rate, early onset of sexual maturity and high fecundity are probably responsible for the rapid spread of G. tigrinus throughout much of the Netherlands.     

Japanese Hollies: Intolerant Hosts of Meloidogyne arenaria in Microplots

Japanese hollies were itttolerant of Meloidogyne arenaria in field microplot experiments. Ilex crenata var. rotundifolia was relatively more tolerant than I. crenata var. convexa or I. crenata var. helleri. When M. arenaria was added at various itfitial population densities to soil containing plants of "Helleri," "Convexa," and "Rotundifolia," respectively, 91, 75, and 25% were killed by the end of the third growing season. No control plants died during the same period. Initial numbers of M. arenaria larvae and eggs were the only population densities that were correlated (negatively), regardless of cultivar, with plant growth over the three growing seasons. A linear relation was found for initial density of M. arenaria and growth of I. crenata rotundifolia. Increasing nematode density by 10-fold suppressed the growth of this cultivar by 23%.