Structure characterization of the central repetitive domain of high molecular weight gluten proteins. I. Model studies using cyclic and linear peptides.

The high molecular weight (HMW) proteins from wheat contain a repetitive domain that forms 60-80% of their sequence. The consensus peptides PGQGQQ and GYYPTSPQQ form more than 90% of the domain; both are predicted to adopt beta-turn structure. This paper describes the structural characterization of these consensus peptides and forms the basis for the structural characterization of the repetitive HMW domain, described in the companion paper. The cyclic peptides cyclo-[PGQGQQPGQGQQ] (peptide 1), cyclo-[GYYPTSPQQGA] (peptide 2), and cyclo-[PGQGQQGYYPTSPQQ] (peptide 3) were prepared using a novel synthesis route. In addition, the linear peptides (PGQGQQ)n (n = 1, 3, 5) were prepared. CD, FTIR, and NMR data demonstrated a type II beta-turn structure at QPGQ in the cyclic peptide 1 that was also observed in the linear peptides 9PGQGQQ)n. A type I beta-turn was observed at YPTS and SPQQ in peptides 2 and 3, with additional beta-turns of either type I or II at GAGY (peptide 2) and QQGY (peptide 3). The proline in YPTS showed considerable cis/trans isomerization, with up to 50% of the population in the cis-conformation; the other prolines were more than 90% in the trans conformation. The conversion from trans to cis destroys the type I beta-turn at YPTS, but leads to an increase in turn character at SPQQ and GAGY (peptide 2) or QQGY (peptide 3).     

四川自贡大山铺成渝龟科—新属

描述了产自四川自贡大山铺恐龙化石坑中的三件龟甲标本,命名为一新属新种—周氏四川龟（Sichuanchelyschowigen．etsp．nov．）。该属以椎盾极横宽,中部缘盾极狭长为主要特征,它代表了成渝龟科中一类较特别的类型。     

Protein secondary structure of the isolated photosystem II reaction center and conformational changes studied by Fourier transform infrared spectroscopy.

The secondary structure of the photosystem II (PSII) reaction center isolated from pea chloroplasts has been characterized by Fourier transform infrared (FTIR) spectroscopy. Spectra were recorded in aqueous buffers containing H2O or D2O; the detergent present for most measurements was dodecyl maltoside. The broad amide I and amide II bands were analyzed by using second-derivative and deconvolution procedures. Absorption bands were assigned to the presence of alpha-helices, beta-sheets, turns, or random structure. Quantitative analysis revealed that this complex contained a high proportion of alpha-helices (67%) and some antiparallel beta-sheets (9%) and turns (11%). An irreversible decrease in the intensity of the band associated with the alpha-helices occurs upon exposure of the isolated PSII reaction center to bright illumination. This loss of alpha-helical content gave rise to an increase in other secondary structures, particularly beta-sheets. After similar pretreatment with light, sodium dodecyl sulfate polyacrylamide gel electrophoresis reveals lower mobility and solubility of constituent D1 and D2 polypeptides of the PSII reaction center. Some degradation of these polypeptides also occurs. In contrast, there is no change in the mobility of the two subunits of cytochrome b559. In the absence of illumination, the PSII reaction center exchanged into dodecyl maltoside shows good thermal stability as compared with samples in Triton X-100. Only at a temperature of about 60 degrees C do spectral changes take place that are indicative of denaturation.     

Conformational transition between native and reactive center cleaved forms of alpha 1-antitrypsin by Fourier transform infrared spectroscopy and small-angle neutron scattering

alpha 1-Antitrypsin (alpha 1-AT) is the best-characterized member of the serpin superfamily of plasma proteins. Protease inhibitor members of this family undergo a characteristic reactive-center cleavage during expression of their inhibitory activity. The physical basis of this transition in alpha 1-AT from the stressed native conformation to the more stable reactive center cleaved (split) form was studied by Fourier transform infrared (FT-IR) spectroscopy and neutron scattering. The FT-IR spectra show that, while split alpha 1-AT has three intense well-resolved components associated with the presence of antiparallel beta-sheet and alpha-helix conformations, the amide I band of native alpha 1-AT has only one intense component, associated with the presence of beta-sheet structure. 1H-2H exchange within the polypeptide backbone, studied by FT-IR and NMR spectroscopy, shows that the native form undergoes greater exchange than the split form. Under the same conditions, neutron scattering shows no differences in the radius of gyration RG of the native and the split forms. In contrast, in high concentrations of phosphate approaching those used for crystallization, the native form (unlike the split form) undergoes dimerization. These data indicate that the conformational transition largely involves localized secondary and tertiary structure rearrangements. We propose that the energetically stressed native alpha 1-AT structure is the consequence of a significantly reduced number of hydrogen bonds in secondary structure components and that reactive-site cleavage between Met358 and Ser359 is the key for the development of the fully hydrogen bonded more stable serpin structure.     

Ant versus bird exclusion effects on the arthropod assemblage of an organic citrus grove

1. Predation‐exclusion experiments have highlighted that top‐down control is pervasive in terrestrial communities, but most of these experiments are simplistic in that they only excluded a single group of predators and the effect of removal was evaluated on a few species from the community. The main goal of our study was to experimentally establish the relative effects of ants and birds on the same arthropod assemblage of canopy trees. 2. We conducted 1‐year long manipulative experiments in an organic citrus grove intended to quantify the independent effects of bird and ant predators on the abundance of arthropods. Birds were excluded with plastic nets whereas ants were excluded with sticky barriers on the trunks. The sticky barrier also excluded other ground dwelling insects, like the European earwig Forficula auricularia L. 3. Both the exclusion of ants and birds affected the arthropod community of the citrus canopies, but the exclusion of ants was far more important than the exclusion of birds. Indeed, almost all groups of arthropods had higher abundance in ant‐excluded than in control trees, whereas only dermapterans were more abundant in bird‐excluded than in control trees. A more detailed analysis conducted on spiders also showed that the effect of ant exclusion was limited to a few families rather than being widespread over the entire diverse spectrum of spiders. 4. Our results suggest that the relative importance of vertebrate and invertebrate predators in regulating arthropod populations largely depends on the nature of the predator–prey system.     

Urinary and Dietary Analysis of 18,470 Bangladeshis Reveal a Correlation of Rice Consumption with Arsenic Exposure and Toxicity

Background

We utilized data from the Health Effects of Arsenic Longitudinal Study (HEALS) in Araihazar, Bangladesh, to evaluate the association of steamed rice consumption with urinary total arsenic concentration and arsenical skin lesions in the overall study cohort (N=18,470) and in a subset with available urinary arsenic metabolite data (N=4,517).

Methods

General linear models with standardized beta coefficients were used to estimate associations between steamed rice consumption and urinary total arsenic concentration and urinary arsenic metabolites. Logistic regression models were used to estimate prevalence odds ratios (ORs) and their 95% confidence intervals (CIs) for the associations between rice intake and prevalent skin lesions at baseline. Discrete time hazard models were used to estimate discrete time (HRs) ratios and their 95% CIs for the associations between rice intake and incident skin lesions.

Results

Steamed rice consumption was positively associated with creatinine-adjusted urinary total arsenic (β=0.041, 95% CI: 0.032-0.051) and urinary total arsenic with statistical adjustment for creatinine in the model (β=0.043, 95% CI: 0.032-0.053). Additionally, we observed a significant trend in skin lesion prevalence (P-trend=0.007) and a moderate trend in skin lesion incidence (P-trend=0.07) associated with increased intake of steamed rice.

Conclusions

This study suggests that rice intake may be a source of arsenic exposure beyond drinking water.     

Beyond average protein secondary structure content prediction using FTIR spectroscopy

This paper demonstrates that secondary structure information beyond purely protein secondary structure content can be predicted from FTIR (Fourier transform infrared spectroscopy) spectra of proteins with a high degree of accuracy. Both neural networks and adaptive neuro-fuzzy inference systems (ANFISs) were employed to predict helix/sheet segment information. The best results were achieved using ANFISs with fuzzy subtractive clustering based on normalised, compressed amide I data with an average SEP (standard error of prediction, root mean of squared errors) of 1.51. Predictions for average helix/sheet length based merely on the amide I band maximum position in combination with the full-width at half-height resulted in a comparable average SEP of 1.62. This suggests the importance of information on the position and width of the amide I band maximum for the prediction of helix/sheet segment information. Finally, the most promising pattern recognition approaches found in this study were applied to a protein with an as yet unknown x-ray structure: native a1-antichymotrypsin (a1-ACT).     

Synthetic Peptide Fragments as Probes for Structure Determination of Potassium Ion-Channel Proteins

Potassium channels are a diverse class of transmembrane proteins that are responsible for diffusion of potassium ion across cell membranes. The lack of large quantities of these proteins from natural sources, is a major hindrance in their structural characterization using biophysical techniques. Synthetic peptide fragments corresponding to functionally important domains of these proteins provide an attractive approach towards characterizing the structural organization of these ion-channels. Conformational properties of peptides from three different potassium channels (Shaker, ROMK1 and minK) have been characterized in aqueous media, organic solvents and in phospholipid membranes. Techniques used for these studies include FTIR, CD and 2D-NMR spectroscopy. FTIR spectroscopy has been a particularly valuable tool for characterizing the folding of the ion-channel peptides in phospholipid membranes; the three different types of potassium channels all share a common transmembrane folding pattern that is composed of a predominantly -helical structure. There is no evidence to suggest the presence of any significant -sheet structure. These results are in excellent agreement with the crystal structure of a bacterial potassium channel (Doyle, D. A. et al. (1998) Science 280:69–77), and suggest that all potassium channel proteins may share a common folding motif where the ion-channel structure is constructed entirely from -helices.