Computer modeling of δ opioid receptor and interaction with ligands

Summary Human σ opioid receptor (σOR), a G-protein-coupled receptor, has been modeled using the helix axes as revealed by the crystallographic structure of bacteriorhodopsin and ligand binding profiles of single-point mutants of σOR. The model revealed feasibility of existence of a second disulfide bridge between the transmembrane helices (TMHs) 6 and 7, Cys²⁷³-Cys³⁰³. A common binding site has been suggested for high-affinity selective agonists DPDPE, DPLPE, DTLET, BW373U86 and antagonist Naltrindole. Docking calculations have shown that the amino group of the ligands forms a hydrogen bond with the imidazole ring of His³⁰¹ (TMH7) rather than with Asp¹²⁸ (TMH3) and is not a cation counterpart of this highly conserved aspartyl residue. All the findings and the model shed light on the putative structure and functioning of opioid receptors and can be used for designing further mutagenesis experiments.     

α-Bn-o-AMPA as a cis peptide bond mimic in somatostatin analogues

Summary In a previous communication we reported the racemic synthesis of the cis peptide bond mimic α-benzyl-o-aminomethylphenylacetic acid and its incorporation in the cyclic somatostatin analoguesc[α(R andS)Bn-o-AMPA-Phe⁷-d-Trp⁸-Lys⁹-Thr¹⁰]. Since the epimeric peptides exhibit different binding affinities, we completed the structure-activity study with an asymmetric synthesis. A model for the solution conformation ofc[α(R andS)Bn-o-AMPA-Phe⁷-d-Trp⁸-Lys⁹-Thr¹⁰] is proposed on the basis of a 2D NMR study in CD₃OH and restrained molecular dynamics.     

Molecular Modeling of the NPY Binding Site on the Y1 Receptor

A three-dimensional model of the neuropeptide Y (NPY) - rat Y₁ (rY₁) receptor complex and of the NPY _13-36 - rY₁ receptor complex was constructed by molecular modeling based on the electron density projection map of rhodopsin and on site-directed mutagenesis studies of neuropeptide receptors. In order to further guide the modeling, the nucleotide sequences encoding Trp287, Cys295 and His297 in the third extracellular loop of the rY₁ receptor, were altered by site-directed mutagenesis experiments. Single-point mutated receptors were expressed in COS-7 cells, and tested for their ability to bind radio labelled NPY (³H-NPY). Mutations of Trp287 and His297 completely abolished binding of ³H-NPY. The Cys295Ser mutation only slightly decreased the binding of ³H-NPY, suggesting that the involvement of Cys295 in a disulphide bond is not essential for maintaining the correct three-dimensional structure of the binding site for NPY. Molecular dynamics simulations of NPY-rY₁ receptor interactions suggested that Asp199, Asp103 and Asp286 in the receptor interact, respectively, with Lys4, Arg33 and Arg35 of NPY. The simulations also suggested that His297 acts as a hydrogen acceptor from Arg35 in NPY, and that Tyr1 of NPY interacts with a binding pocket on the receptor formed by Asn115, Asp286, Trp287 and His297. Tyr36 in NPY interacted both with Thr41 and Tyr99 via hydrogen bonds, and also with Asn296, His297 and Phe301. The present study suggests that amino acid residues at the extracellular end of the transmembrane helices and in the extracellular loops are strongly involved in binding to NPY and NPY_13-36.Electronic Supplementary Material available.     

Oscillations of the energy gap for the initial electron-transfer step in bacterial reaction centers

Oscillations in the electrostatic energy gap [V_elec(t)] for electron transfer from the primary electron donor (P) to the adjacent bacteriochlorophyll (B) in photosynthetic bacterial reaction centers are examined by molecular-dynamics simulations. Autocorrelation functions of V_elec in the reactant state (PB) include prominent oscillations with an energy of 17 cm^–1. This feature is much weaker if the trajectory is propagated in the product state P⁺B^–. The autocorrelation functions also include oscillations in the regions of 5, 80 and 390 cm^–1 in both states, and near 25 and 48 cm^–1 in P⁺B^–. The strong 17-cm^–1 oscillation could involve motions that modulate the distance between P and B, because a similar oscillation occurs in the direct electrostatic interactions between the electron carriers.     

Dynamic and structural properties of glucose oxidase enzyme

The catalytic oxidation of β-D-glucose by the enzyme glucose oxidase involves a redox change of the flavin coenzyme. The structure and the dynamics of the two extreme glucose oxidase forms were studied by using infrared absorption spectroscopy of the amide I′ band, tryptophan fluorescence quenching and hydrogen isotopic exchange. The conversion of FAD to FADH₂ does not change the amount of α-helix present in the protein outer shell, but reorganises a fraction of random coil to β-sheet structure. The dynamics of the protein interior vary with the redox states of the flavin without affecting the motions of the structural elements near the protein surface. From the structure of glucose oxidase given by X-ray crystallography, these results suggest that the dynamics of the interface between the two monomers are involved in the catalytic mechanism. Received: 27 December 1996 / Accepted: 18 July 1997     

广布中剑水蚤对裸腹和秀体的摄食(英文)

１９９５年６月至９月,在武汉东湖,通过摄食实验和野外调查,作者研究了广布中剑水蚤对裸腹和秀体的摄食。研究结果证实,广布中剑水蚤能够抓取和摄食裸腹和秀体。广布中剑水蚤对小型裸腹的平均摄食率高于大型裸腹。多重统计分析结果表明,广布中剑水蚤对小型和大型裸腹的摄食率有显著差异（Ｐ＝００３３５）,捕食者喜食小型猎物。由于广布中剑水蚤的摄食习性,它对裸腹和秀体的种群动态有重要影响,但随着鱼产量增加,广布中剑水蚤对猎物摄食的影响效果被减弱了。     

Bird diversity: a predictable function of satellite-derived estimates of seasonal variation in canopy light absorbance across the United States

Aim  To investigate the relationships between bird species richness derived from the North American Breeding Bird Survey and estimates of the average, minimum, and the seasonal variation in canopy light absorbance (the fraction of absorbed photosynthetically active radiation, fPAR) derived from NASA's Moderate Resolution Imaging Spectroradiometer (MODIS).
Location  Continental USA.
Methods  We describe and apply a 'dynamic habitat index' (DHI), which incorporates three components based on monthly measures of canopy light absorbance through the year. The three components are the annual sum, the minimum, and the seasonal variation in monthly fPAR, acquired at a spatial resolution of 1 km, over a 6-year period (2000–05). The capacity of these three DHI components to predict bird species richness across 84 defined ecoregions was assessed using regression models.
Results  Total bird species richness showed the highest correlation with the composite DHI [ R ² = 0.88, P  < 0.001, standard error of estimate (SE) = 8 species], followed by canopy nesters ( R ² = 0.79, P  < 0.001, SE = 3 species) and grassland species ( R ² = 0.74, P  < 0.001, SE = 1 species). Overall, the seasonal variation in fPAR, compared with the annual average fPAR, and its spatial variation across the landscape, were the components that accounted for most ( R ² = 0.55–0.88) of the observed variation in bird species richness.
Main conclusions  The strong relationship between the DHI and observed avian biodiversity suggests that seasonal and interannual variation in remotely sensed fPAR can provide an effective tool for predicting patterns of avian species richness at regional and broader scales, across the conterminous USA.     

Effects of European colonization on indigenous ecosystems: post-settlement changes in tree stand structures in Eucalyptus–Callitris woodlands in central New South Wales, Australia

Aim There has been considerable debate about pre‐settlement stand structures in temperate woodlands in south‐eastern Australia. Traditional histories assumed massive tree losses across the region, whereas a number of recent histories propose that woodlands were originally open and trees regenerated densely after settlement. To reconcile these conflicting models, we gathered quantitative data on pre‐settlement stand structures in Eucalyptus–Callitris woodlands in central New South Wales Australia, including: (1) tree density, composition, basal area and canopy cover at the time of European settlement; and (2) post‐settlement changes in these attributes. Location Woodlands dominated by Eucalyptus species and Callitris glaucophylla, which originally occupied approximately 100,000 km² in central New South Wales, Australia. Methods We recorded all evidence of pre‐settlement trees, including stumps, stags and veteran trees, from 39 relatively undisturbed 1‐ha stands within 16 State Forests evenly distributed across the region. Current trees were recorded in a nested 900 m² quadrat at each site. Allometric relationships were used to estimate girth over bark at breast height, tree basal area, and crown diameter from the girth of cut stumps. A post‐settlement disturbance index was developed to assess correlations between post‐settlement disturbance and attributes of pre‐settlement stands. Results The densities of all large trees (> 60 cm girth over bark at breast height) were significantly greater in current stands than at the time of European settlement (198 vs. 39 trees ha^?1). Pre‐settlement and current stands did not differ in basal area. However, the proportional representation of Eucalyptus and Callitris changed completely. At the time of settlement, stands were dominated by Eucalyptus (78% of basal area), whereas current stands are dominated by Callitris (74%). On average, Eucalyptus afforded 83% of crown cover at the time of settlement. Moreover, the estimated density, basal area and crown cover of Eucalyptus at the time of settlement were significantly negatively correlated with post‐settlement disturbance, which suggests that these results underestimate pre‐settlement Eucalyptus representation in the most disturbed stands. Main conclusions These results incorporate elements of traditional and recent vegetation histories. Since European settlement, State Forests have been transformed from Eucalyptus to Callitris dominance as a result of the widespread clearance of pre‐settlement Eucalyptus and dense post‐settlement recruitment of Callitris. Tree densities did increase greatly after European settlement, but most stands were much denser at the time of settlement than recent histories suggest. The original degree of dominance by Eucalyptus was unexpected, and has been consistently underestimated in the past. This study has greatly refined our understanding of post‐settlement changes in woodland stand structures, and will strengthen the foundation for management policies that incorporate historical benchmarks of landscape vegetation changes.     

Evaluation of antral follicle growth in the macaque ovary during the menstrual cycle and controlled ovarian stimulation by high‐resolution ultrasonography

To date, ultrasonography of monkey ovaries is rare and typically of low resolution. The objectives of this study were to use state‐of‐the‐art, high‐resolution, transabdominal ultrasonography with real‐time Doppler capabilities to: (1) determine whether one can reliably detect in real time the large dominant follicle, the corpus luteum (CL), and small (<2 mm) antral follicles on the ovaries of rhesus monkeys during the natural menstrual cycle; and (2) predict the follicular response of rhesus ovaries to controlled ovarian stimulation (COS) protocols. Rhesus monkeys were selected for transabdominal ultrasonography using a GE Voluson 730 Expert Doppler System at discrete stages of the menstrual cycle. Subsequently, serial ultrasound scanning was employed to observe growth of antral follicles and the CL. Finally, females were scanned to assess follicular growth during COS. The dominant structure and small antral follicles (<2 mm) were reliably visualized in real time. The follicle destined to ovulate could be identified by size differential by day 3 of the follicular phase. The number of small antral follicles present before onset of COS protocol correlated positively with the number of metaphase II‐stage oocytes collected after treatment. The results of this study demonstrate that the population dynamics of antral follicle pools can be noninvasively evaluated in monkeys during natural and pharmacologic ovarian cycles. Am. J. Primatol. 71:384–392, 2009. © 2009 Wiley‐Liss, Inc.