Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling

Although protein Z (PZ) has a domain arrangement similar to the essential coagulation proteins FVII, FIX, FX, and protein C, its serine protease (SP)-like domain is incomplete and does not exhibit proteolytic activity. We have generated a trial sequence of putative activated protein Z (PZa) by identifying amino acid mutations in the SP-like domain that might reasonably resurrect the serine protease catalytic activity of PZ. The structure of the activated form was then modeled based on the proposed sequence using homology modeling and solvent-equilibrated molecular dynamics simulations. In silico docking of inhibitors of FVIIa and FXa to the putative active site of equilibrated PZa, along with structural comparison with its homologous proteins, suggest that the designed PZa can possibly act as a serine protease.     

水稻品种对稻纵卷叶螟抗性的物理及生化机制

稻纵卷叶螟Cnaphalocrocis medinalis连年大发生,为在其治理中培育和推广抗虫品种,本文应用扫描电镜和生化测定研究了5个常用水稻栽培品种扬辐粳8号、扬稻6号、扬粳9538、淮稻9号和宁梗1号叶片中的硅含量、硅颗粒大小、蜡质含量等物理指标和一些生化指标与抗虫性的关系,并比较了稻纵卷叶螟幼虫危害不同水稻品种后其体内生化反应的差异。结果表明抗虫品种宁梗1号、淮稻9号叶片表面的硅含量显著高于感虫品种,硅颗粒大小在品种间无显著差异。宁粳1号叶片蜡质含量显著高于其他品种。由此表明叶片表面硅和蜡质含量与抗性有关。稻纵卷叶螟幼虫取食后,抗虫品种体内的过氧化物酶（POD）、超氧化物岐化酶（SOD）活性显著高于感虫品种,但丙二醛(MDA)含量低于感虫品种。稻纵卷叶螟幼虫取食不同品种后,其体内一些酶的活性明显不同,取食抗虫品种的幼虫体内POD和谷胱甘肽-S-转移酶(GST)活性显著高于取食其他品种的幼虫,SOD活性显著低于取食感虫品种的幼虫, 表明抗虫品种对稻纵卷叶螟幼虫有毒害作用。     

Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines

Theoretical microscopic titration curves (THEMATICS) is a computational method for the identification of active sites in proteins through deviations in computed titration behavior of ionizable residues. While the sensitivity to catalytic sites is high, the previously reported sensitivity to catalytic residues was not as high, about 50%. Here THEMATICS is combined with support vector machines (SVM) to improve sensitivity for catalytic residue prediction from protein 3D structure alone. For a test set of 64 proteins taken from the Catalytic Site Atlas (CSA), the average recall rate for annotated catalytic residues is 61%; good precision is maintained selecting only 4% of all residues. The average false positive rate, using the CSA annotations is only 3.2%, far lower than other 3D-structure-based methods. THEMATICS-SVM returns higher precision, lower false positive rate, and better overall performance, compared with other 3D-structure-based methods. Comparison is also made with the latest machine learning methods that are based on both sequence alignments and 3D structures. For annotated sets of well-characterized enzymes, THEMATICS-SVM performance compares very favorably with methods that utilize sequence homology. However, since THEMATICS depends only on the 3D structure of the query protein, no decline in performance is expected when applied to novel folds, proteins with few sequence homologues, or even orphan sequences. An extension of the method to predict non-ionizable catalytic residues is also presented. THEMATICS-SVM predicts a local network of ionizable residues with strong interactions between protonation events; this appears to be a special feature of enzyme active sites.     

The AutoDock suite at 30

The AutoDock suite provides a comprehensive toolset for computational ligand docking and drug design and development. The suite builds on 30 years of methods development, including empirical free energy force fields, docking engines, methods for site prediction, and interactive tools for visualization and analysis. Specialized tools are available for challenging systems, including covalent inhibitors, peptides, compounds with macrocycles, systems where ordered hydration plays a key role, and systems with substantial receptor flexibility. All methods in the AutoDock suite are freely available for use and reuse, which has engendered the continued growth of a diverse community of primary users and third‐party developers.     

不同农田生态系统土壤碳库管理指数的研究

讨论不同农田生态系统的土壤活性碳库和碳库管理（ＣＰＭＩ）,结果表明,不同农田生态系统的土壤ＣＰＭＩ明显受施肥、气候、土壤利用方式,耕种年限等因素的影响。供试土壤的活性碳含量范围为０．４９～４．９９ｍｇ／ｇ,土壤ＣＰＭＩ为５１．６～１６５。不同施肥地红壤ＣＰＭＩ的影响顺序为绿肥（ＧＭ）〉概肥（ＦＹＭ）〉ＦＹＭ－ＮＰＤ〉参考（ＲＥＦ）〉ＮＰＫ〉对照（ＣＫ）,在水稻土中,共相应的影响顺序为,稻草（ＲＳＣ     

曲霉属真菌活性代谢产物及在农业生产中的应用研究进展

曲霉属(Aspergillus)真菌是一类分布广泛的丝状真菌,种类繁多,代谢产物丰富,应用广泛,在农业、医药、生物能源、化妆品、食品发酵等行业均有应用。对近年来曲霉属真菌活性代谢产物在抗菌、抗氧化、抗病毒方面的研究进展进行了综述。结合实验室研究成果,对近年来曲霉属真菌代谢产物在秸秆腐熟菌剂、溶磷生物菌剂、拮抗植物寄生线虫等农业生产领域中的应用进行综述,以期为开发应用曲霉属真菌活性代谢产物的研究提供参考。     

阳西静容卫矛(卫矛科)——华南一新变种

报道了中国广东省阳西县沟谷雨林内1新变种——阳西静容卫矛(Euonymus chengii var.yangxiensis Y.S.Ye&L.F.Wu),并提供简要描述和照片。阳西静容卫矛隶属于卫矛科(Celastraceae)浅裂卫矛组(Euonymus),蒴果顶端浅裂,与原变种静容卫矛(E.chengii J.S.Ma)和中华卫矛(E.nitidus Benth.)相似,主要区别是该变种叶缘顶部2/3以上具锯齿,侧脉明显,花少且大,蒴果大,萼片伸展。     

宁夏国外小麦种质资源考察、引进和利用

国外小麦种质资源引进在宁夏小麦引种中发挥着重要的作用。碧玉麦、阿勃、墨卡(卡杰姆F-71)、WC-20(宁春37)、9186(宁冬6号)等国外小麦品种在宁夏生产上直接利用。宁夏春小麦的品质杂交选育始于1953年,利用国外小麦种质资源先后培育出斗地1号、宁春4号等50余个春麦品种。1990年宁夏国外冬麦种质资源的引进带动了宁夏引黄灌区冬麦北移和耕作改制的研究,也引发了宁夏冬麦品种杂交选育的研究。宁夏引黄灌区冬小麦品种的杂交选育的工作始于1991年,经过15年的努力,杂交选育出第一批冬麦品种宁冬10号、宁冬11号,2010年在冬麦生产上取代了明丰5088,不仅实现了宁夏引黄灌区冬小麦品种第3次更新、实现了小麦品种的5次更新,而且使宁夏小麦生产水平跃上新台阶,有力地促进宁夏引黄灌区耕作制度改善和种植业结构的调整。     

Formulation of a coupled mechanism between solute diffusion,phosphatase-kinase reactions and membrane potentials for the primary active transport of phosphorylated substrates through biological membranes

Coupled interrelations occurring between a phosphatase/kinase reaction sequence acting in unstirred layers and on both sides of a charged biomembrane pore structure are presented as a plausible kinetic model for the primary active transport of phosphorylated molecules. Simulations conducted at the cell level and with credible numerical values demonstrate that the enzymes positions strongly regulate the membrane permeability for the transported substrate. Depending on both the enzymes positions (more or less far from the membrane) and the membrane charges, the membrane may appear either impervious, either permeable or able to actively transport a phosphorylated substrate. Globally all happens as if, in function of the enzymes positions, a permanent pore may be regulated, changing from a more closed to a more open conformation.