Reduced state transition barrier of CDK6 from open to closed state induced by Thr177 phosphorylation and its implication in binding modes of inhibitors

Background

CDK6 is considered as a highly validated anticancer drug target due to its essential role in regulating cell cycle progression at G1 restriction point. Activation of CDK6 requires the phosphorylation of Thr177 on A-loop, but the structural insights of the activation mechanism remain unclear.

Tchebichef image moment approach to the prediction of protein secondary structures based on circular dichroism

Circular dichroism (CD) spectroscopy is a widely used technique for the evaluation of protein secondary structures that has a significant impact for the understanding of molecular biology. However, the quantitative analysis of protein secondary structures based on CD spectra is still a hard work due to the serious overlap of the spectra corresponding to different structural motifs. Here, Tchebichef image moment (TM) approach is introduced for the first time, which can effectively extract the chemical features in CD spectra for the quantitative analysis of protein secondary structures. The proposed approach was applied to analyze reference set and the obtained results were evaluated by the strict statistical parameters such as correlation coefficient, cross‐validation correlation coefficient and root mean squared error. Compared with several specialized prediction methods, TM approach provided satisfactory results, especially for turns and unordered structures. Our study indicates that TM approach can be regarded as a feasible tool for the analysis of the secondary structures of proteins based on CD spectra. An available TMs package is provided and can be used directly for secondary structures prediction.     

Design of nonapeptide LVFFARKHH: A bifunctional agent against Cu2+‐mediated amyloid β‐protein aggregation and cytotoxicity

Dysfunctional accumulation of amyloid β‐protein (Aβ) mediated by Cu²⁺ exhibits higher neurotoxicity and accelerates the progress of Alzheimer's disease, so inhibition of Cu²⁺‐mediated Aβ aggregation and cytotoxicity has been considered as a therapeutic strategy for the disease. Herein, a nonapeptide was designed by linking HH to the C‐terminus of a peptide inhibitor of Aβ aggregation, LVFFARK (LK7). We found that the nonapeptide, LK7‐HH, possessed dual functionality, including enhanced inhibition capability on Aβ aggregation as compared to LK7, and chelating Cu²⁺ with a dissociation constant of 5.50 μM. This enabled LK7‐HH to arrest the generation of reactive oxygen species catalyzed by Cu²⁺ or Cu²⁺‐Aβ complex, and to inhibit Cu²⁺‐induced Aβ aggregation. Moreover, in contrast with the cytotoxicity of LK7 aggregates, LK7‐HH was biocompatible because HH conjugation made its aggregation behavior different from LK7. Thus, LK7‐HH efficiently suppressed Cu²⁺‐mediated Aβ aggregation and cytotoxicity. An equimolar concentration of LK7‐HH increased cell viability from 50% to 90% when treating Aβ₄₀‐Cu²⁺ complexes. The results provided insights into the roles of HH in enhancing the inhibition of Aβ and Cu²⁺‐induced Aβ aggregations, in eliminating Cu²⁺‐induced cytotoxicities by arresting generation of reactive oxygen species, and in making the peptide biocompatible. Therefore, this work would contribute to the design of potent peptide‐based inhibitors of Cu²⁺‐mediated Aβ aggregation and cytotoxicity.     

三维基因组数据分析方法进展

对染色质三维结构的探究逐渐成为了解基因组功能与基因调控关系的必要手段.近年来,随着高通量染色体构象捕获(Hi-C)等技术的发展和高通量测序成本的降低,全基因组交互作用的数据量快速增长,交互作用图谱分辨率不断提高.这给三维基因组学发展带来机遇的同时,也给计算建模带来了挑战.当前,三维基因组数据的分析方法覆盖面广,包括了数据前期处理、标准化、可视化、特征提取、三维建模等环节,但是如何从中选择高效、准确的方法却成为制约研究者们开展研究的一项关键因素.本文根据这些方法的适用场景、原理及特点进行系统地归纳,并重点关注了针对新技术或新需求的分析方法,以期促进这一领域中信息学方法的应用和开发,助力三维基因组学的研究.     

文心兰乙烯不敏感基因EIN2的克隆及表达分析

该研究采用PCR、RACE方法,对文心兰‘南茜’的乙烯不敏感蛋白基因（ethylene insensitive 2,EIN2）进行克隆及生物信息学分析,并采用qRT PCR技术,对该基因在文心兰不同组织器官和不同花期中的表达模式进行分析。结果表明：（1）成功克隆得到文心兰_EIN2基因序列,命名为OnEIN2（MH497388）;该基因cDNA序列全长为4 177 bp,其中开放阅读框3 879 bp,编码1 292个氨基酸,3′非编码区长208 bp,5′非编码区长90 bp。（2）生物信息学分析显示OnEIN2是一个不稳定的疏水蛋白,含有跨膜结构,分子式为C₆₄₀₆H₉₉₈₈N₁₆₇₀O₁₈₉₇S₄₇;蛋白质分子量142.22 kD,理论等电点5.80。多序列比对和系统进化分析表明,文心兰EIN2与铁皮石斛EIN2的相似度最高（81.98%）,二者亲缘关系也最为接近。（3）实时荧光定量PCR分析发现,OnEIN2基因在根、茎、叶花中均有表达,在花中表达量最高,茎中表达量最低;而在不同花期中,盛开期表达量最高,其次是衰老期。研究表明,文心兰OnEIN2基因在开花和衰老过程中可能有重要的作用。     

Isolation and functional characterization of two 5-<Emphasis Type="Italic">O</Emphasis>-glucosyltransferases related to anthocyanin biosynthesis from <Emphasis Type="Italic">Freesia hybrida</Emphasis>

Kelussia odoratissima Mozaff. (or Kelus) is a medicinal plant native to the Zagros Mountains in Iran. This plant is widely used as a food flavoring and for its health-promoting properties. It has been considered an endangered species by the United Nations Development Programme. In this study, a somatic embryogenesis (SE) method was developed for mass propagation of Kelus. The green globular embryogenic callus was induced on cotyledonary leaves using the Murashige and Skoog (MS) medium supplemented with 1 mg/l 2,4-dichlorophenoxyaceticacid (2,4-D) and 0.25 mg/l Kinetin. Different treatments were assayed for proliferation of the embryogenic callus. The calli remained embryogenic in an MS medium containing 2,4-D (1 mg/l). The light treatments and carbon source showed significant effects (P?≤?0.05) on the proliferation and development of somatic embryos. These treatments improved the conversion rate of the cotyledonary-stage embryos by 100%. The average numbers of embryos in the globular, heart, torpedo, and cotyledonary stages decreased by the addition of 3 g/l case in hydrolisate. The genetic stability among tissue culture-derived plants and the mother plant were assessed using the amplification fragment length polymorphism. No polymorphic band was observed among all the plants, exhibiting the genetic stability during in vitro multiplication. This research provides a promising approach for true-to-type plant multiplication of K. odoratissima through SE.     

CipA-mediating enzyme self-assembly to enhance the biosynthesis of pyrogallol in Escherichia coli

Pyrogallol is a valuable phenolic compound and displays various physiological and pharmaceutical functions. Chemical synthesis of pyrogallol suffered from many issues, including environmental pollution, high cost, and low yield. Here, to address the above drawbacks, an artificial pathway for de novo pyrogallol production was established and this pathway only needed two exogenous enzymes (Y385F/T294A PobA and 3,4-dihydroxybenzoic acid decarboxylase (PDC)). Y385F/T294A PobA is a mutant of PobA which is a hydroxylase from Pseudomonas aeruginosa, while PDC is a decarboxylase from Klebsiella pneumoniae subsp. pneumoniae. First, the conversion efficiency of PDC was tested and 1800 ± 100 mg/L pyrogallol was generated from 4 g/L gallic acid (GA). Subsequently, assembly of the whole pathway enabled 33 ± 6 mg/L pyrogallol production from simple carbon sources. After that, based on the assembling property of CipA (a hydrophobic protein) and to enhance the hydroxylation of 3,4-dihydroxybenzoic acid, CipA was employed to organize its fusion (Y385F/T294A PobA) into protein crystalline inclusions (PCIs). Remarkably, the formation of CipA-Y385F/T294A PobA PCIs increased the pyrogallol production to 60 ± 6 mg/L, a 1.8 ± 0.4-fold higher value as compared to the strain without enzyme self-assembly. Additionally, the titer of pyrogallol was enhanced to 80 ± 1 mg/L through yeast extract concentration optimization. This work not only realizes the biosynthesis of pyrogallol from renewable carbon sources but also demonstrates that using CipA-mediating enzyme self-assembly could reinforce the hydroxylation efficiency of Y385F/T294A PobA, resulting in the enhancement of pyrogallol production.

     

Engineered commensal bacteria prevent systemic inflammation-induced memory impairment and amyloidogenesis via producing GLP-1

Applied Microbiology and Biotechnology - The anti-obesity drug GLP-1 has been proven to have an impact on central nervous system, while its extremely short half-life greatly limited its use. In...     

Response of dominant grassland species in the temperate steppe of Inner Mongolia to different land uses at leaf and ecosystem levels

In order to study the responses of dominant species to different land uses in the semiarid temperate grassland of Inner Mongolia, we tested the physiological responses of Stipa grandis, Leymus chinensis, and Artemisia frigida to mowing, grazing exclusion, and grazing land uses at the leaf and ecosystem levels. The grazing-exclusion and mowing sites released CO₂, but the grazing site was a net carbon sink. L. chinensis and S. grandis contributed more to the ecosystem CO₂ exchange than A. frigida. At the grazing-exclusion and mowing sites, Leymus chinensis and Stipa grandis both exhibited a higher light-saturation point and higher maximum photosynthetic rate than that at the grazing site, which increased photosynthesis and growth compared to those at the grazing site. In contrast, A. frigida possessed a higher nitrogen content than the other species, and more of the light energy used for photosynthesis, particularly at the grazing site.