Response of dynamic structure to removal of a disulfide bond: normal mode refinement of C77A/C95A mutant of human lysozyme.

In order to investigate the response of dynamic structure to removal of a disulfide bond, the dynamic structure of human lysozyme has been compared to its C77A/C95A mutant. The dynamic structures of the wild type and mutant are determined by normal mode refinement of 1.5-A-resolution X-ray data. The C77A/C95A mutant shows an increase in apparent fluctuations at most residues. However, most of the change originates from an increase in the external fluctuations, reflecting the effect of the mutation on the quality of crystals. The effects of disulfide bond removal on the internal fluctuations are almost exclusively limited to the mutation site at residue 77. No significant change in the correlation of the internal fluctuations is found in either the overall or local dynamics. This indicates that the disulfide bond does not have any substantial role to play in the dynamic structure. A comparison of the wild-type and mutant coordinates suggests that the disulfide bond does not prevent the 2 domains from parting from each other. Instead, the structural changes are characteristic of a cavity-creating mutation, where atoms surrounding the mutation site move cooperatively toward the space created by the smaller alanine side chain. Although this produces tighter packing, more than half of the cavity volume remains unoccupied, thus destabilizing the native state.     

NMR restraint analysis of transforming growth factor alpha: a key component for NMR structure refinement.

Structures of the protein, transforming growth factor alpha (TGF-alpha), have been derived from NMR data using distance geometry and subsequent energy refinement. Analysis of the sequential NOE distance bounds using a template algorithm provides a check for consistency in the calculation of bounds, stereospecific assignment of prochiral centers, and secondary structure assignment. Application of the template algorithm to the long range NOEs found within the NMR data sets collected at pH 6.3 and pH 3.4 is used to assess the confidence levels for the accuracy of the structures obtained from modeling. The method also provides critical insight in differentiating regions of the structure that are well defined from those that are not. Use of the restraint analysis protocol is shown to be a powerful adjunct to currently used methods for the assignment of protein structures from NMR data.     

Using the biomasses of soil nematode taxa as weighting factors for assessing soil food web conditions

We propose the use of nematode generic biomasses as weighting factors for calculation of nematode community indices. Three data sets were used to calculate the indices using guild-based weighting (i.e., fixed weighting of nematode guilds) and genus-based weighting (i.e., weighting based on the nematode generic biomasses). The genus-based weighting factors were quadratically correlated with guild-based weighting factors, but the genus-based weighting factors were highly variable within each nematode guild, indicating that important information was likely missing when guild-based weighting was used. Although variation patterns of in the indices in response to management practices and land use were often similar for the two weighting systems, they sometimes differed substantially, and the specific index values frequently differed depending on which weighting system was used. In addition, the absolute values of the indices were frequently found to be different between the two weighting systems. Based on the comparison of indices from the two systems, we found that the genus-based system was complementary rather than superior to the guild-based system. It was suggested that both weighting systems should be used for the calculation of the nematode community indices in a study in order to better distinguish the treatment effects.     

New UVA‐emitting BaAlBO3F2:Eu2+ phosphor with PL and TL properties for phototherapy lamp

We present a new phosphor material, BaAlBO₃F₂ doped with Eu²⁺ ions, having emission in the UVA region. The phosphor material is prepared by a simple wet chemical method. Phase confirmation was carried out using the Rietveld refinement program which shows that BaAlBO₃F₂:Eu²⁺ has an hexagonal crystal system. Using a Fourier transform infrared spectroscopy graph, we studied the bond stretching present in the phosphor material. Photoluminescence (PL) characterization, carried out using a RF spectrofluorophotometer, shows two types of PL excitation and emission. Before reduction, emission is in the blue region at 431 nm; after reduction, excitation is at 258 nm and emission is at 361 nm, which is in the UVA region. Some thermoluminescence (TL) studies were carried out in this material for the first time, for example, determination of the trapping parameters, linearity, fading, glow curve convolution and deconvolution (GCCD) function for curve fitting and the T_m–T_stop method for confirmation of the trapped centers in the TL glow peak. Copyright © 2016 John Wiley & Sons, Ltd.     

Capturing the Conformational Ensemble of the Mixed Folded Polyglutamine Protein Ataxin-3

1. Download : Download high-res image (180KB)
2. Download : Download full-size image

     

Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality

1. Download : Download high-res image (136KB)
2. Download : Download full-size image

     

Swift heavy ion induced structural and luminescence characterization of Y2O3:Eu3+ phosphor: a comparative study

We report a comparative study on structural and thermoluminescence modifications of Y₂O₃:Eu³⁺ phosphor induced by 150 MeV Ni⁷⁺, 120 MeV Ag⁹⁺ and 110 MeV Au⁸⁺ swift heavy ions (SHI) in the fluence range 1 × 10¹¹ to 1 × 10¹³ ions/cm². X‐Ray diffraction and transition electron microscopy studies confirm the loss of crystallinity of the phosphors after ion irradiation, which is greater in the case of Au ion irradiation. Structural refinement using the Rietveld method yields the various structural parameters of ion‐irradiated phosphors. Thermoluminescence glow curves of ion‐irradiated phosphors show a small shift in the position of the peaks, along with an increase in intensity with ion fluence. Stopping range of ions in Matter (SRIM) calculations were performed to correlate the change in thermoluminescence properties of various ion‐irradiated phosphors. It shows that the defects created by 110 MeV Au⁸⁺ ions are greater in number. Trapping parameters of ion‐irradiated phosphors were calculated from thermoluminescence data using various glow curve analysis methods. Copyright © 2013 John Wiley & Sons, Ltd.     

黑果枸杞色素的提取和精制工艺研究

本文采用正交实验法对黑果枸杞色素的提取和精制工艺进行了研究。结果表明,黑果枸杞色素的最佳提取条件为:以pH 3.0的80%乙醇作浸提剂,提取温度50℃,提取时间3 h,固液配比1:40;用X-5大孔吸附树脂对色素进行精制,以树脂柱径高比1:15、流速3 mL/minp、H 3.0、色素液浓度1 g/L为最佳吸附条件,色素的吸附量可达0.03715 g/mL湿树脂体积;而以95%乙醇做洗脱液,在pH 2.0、流速5 mL/min、3倍于柱床体积的洗脱液条件下解吸附效果最佳,色素回收率达到97.78%;制取的色素产品外观呈紫红色,色价为36.7。