Changing the binding specificity of a repressor by redesigning an alpha-helix

We replaced amino acids on the 'outside', or solvent-exposed, surface of the DNA recognition alpha-helix of 434 repressor with the corresponding amino acids from the recognition helix of P22 repressor. The binding specificity of the resulting hybrid protein, as measured in vivo and in vitro, was that of P22 repressor.     

侧链型芳香族偶氮基聚氨酯的合成及其液晶态的研究

采取两步法合成侧链型芳香族偶氮基聚氨酯,并应用FT-IR、VPO、DSC和TPOM表征聚氨酯的结构及液晶性。MDI系列聚氨酯由于其主链刚性较大,不出现液晶相,而HDI系列聚氨酯则可出现液晶相,并随着由扩链剂引入主链的“柔性间隔基”的柔性和长度增加,“去偶”作用增强,其液晶相的转变温度和有序性也随之提高。     

Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues

Positively charged amino acids have been shown to be important elements in targeting-peptides that direct proteins into mitochondria, nuclei, and the secretory pathways of both prokaryotic and eukaryotic cells. The 'positive-inside' rule, which observes that regions of polytopic (multi-spanning) membrane proteins facing the cytoplasm are generally enriched in arginyl and lysyl residues whereas translocated regions are largely devoid of these residues, implies that the distribution of positively charged amino acids may also be a major determinant of the transmembrane topology of integral membrane proteins. If this is indeed the case, it should be possible to predictably alter the topology of a polytopic protein by site-directed insertions and/or deletions of positively charged residues in critical locations. I now describe a derivative of Escherichia coli leader peptidase, a polytopic inner-membrane protein, that switches from sec-gene-dependent membrane insertion with a Nout-Cout transmembrane topology to sec-gene-independent insertion with a Nin-Cin topology in response to the addition of four positively charged lysines to its N terminus.     

飞秒激光与硅样品作用生成纳米光栅结构

我们用脉冲宽度120 fs、波长800nm、能量密度从0.1 J/cm2~0.5 J/cm2的激光束照射硅样品和锗硅合金样品表面能够生成各种低维形貌结构。特别是将飞秒激光束散焦至直径为100μm的束斑,并以每秒1000个脉冲照射硅样品表面两秒钟时(能量密度在熔融阈值0.2 J/cm2附近),能生成周期间隔为400nm的浮雕光栅状的一维微结构。我们用飞秒激光与其诱导的等离子体波的相干模型解释了光栅状微结构的形成机理。还发现这种结构有很强的PL发光,PL峰的中心约在719nm处。该飞秒激光加工技术既简捷又稳定,在光学和微电子加工领域应有很好的应用前景。     

带电导体之间的相互作用规律分析

从静电平衡状态下的导体性质出发,详细分析了导体与导体和导体与点电荷之间的相互作用规律,指出了并非同性带电导体一定相互排斥、异性带电导体一定相互吸引的客观规律;利用镜像法详细推证了点电荷与导体球之间的相互作用随距离的变化规律.     

Optimization of specificity in a cellular protein interaction network by negative selection

Most proteins that participate in cellular signalling networks contain modular protein-interaction domains. Multiple versions of such domains are present within a given organism: the yeast proteome, for example, contains 27 different Src homology 3 (SH3) domains. This raises the potential problem of cross-reaction. It is generally thought that isolated domain-ligand pairs lack sufficient information to encode biologically unique interactions, and that specificity is instead encoded by the context in which the interaction pairs are presented. Here we show that an isolated peptide ligand from the yeast protein Pbs2 recognizes its biological partner, the SH3 domain from Sho1, with near-absolute specificity--no other SH3 domain present in the yeast genome cross-reacts with the Pbs2 peptide, in vivo or in vitro. Such high specificity, however, is not observed in a set of non-yeast SH3 domains, and Pbs2 motif variants that cross-react with other SH3 domains confer a fitness defect, indicating that the Pbs2 motif might have been optimized to minimize interaction with competing domains specifically found in yeast. System-wide negative selection is a subtle but powerful evolutionary mechanism to optimize specificity within an interaction network composed of overlapping recognition elements.     

泰比培南侧链合成工艺改进

报道了一种改进的泰比培南侧链合成方法.以苄胺和环氧氯丙烷为起始原料,经取代开环,N-烷基化反应构建四元环分子骨架,该中间体再经氢化、N-叔丁氧羰基化、O-甲烷磺酰化、取代反应、成盐等8步操作合成泰比培南侧链,总收率24.3%.与现有方法相比,反应条件温和,操作简便,试剂廉价易得.     

Enhancing protein C interaction with thrombin results in a clot-activated anticoagulant.

Human protein C is a vitamin K-dependent plasma glycoprotein that circulates as an inactive zymogen. At the endothelial cell surface, thrombin in complex with the integral membrane protein thrombomodulin converts protein C to its active form by specific cleavage of an activation peptide. The activated form of protein C has potent anticoagulant activity as a feedback regulator of thrombin generation (reviewed in refs 4-6), and also has profibrinolytic, anti-ischaemic and anti-inflammatory properties. Protein C is effective in the treatment of model and human thrombotic diseases but, except when it has been used to treat genetic or acquired deficiencies and microvascular thrombosis, it is administered as the activated enzyme, which has a short biological half-life. We have altered two putative inhibitory acidic residues near the thrombin cleavage site, which results in a 30-fold increase in substrate utilization by alpha-thrombin. We combined these changes with a genetically altered glycoform to generate a zymogen protein C with a 60-fold increased cleavage rate by free alpha-thrombin, independent of its cofactor thrombomodulin. We show that this 'proform' of protein C, unlike the natural circulating zymogen, can be activated by thrombin generated in clotting human plasma, resulting in an inhibition of further clot formation. Our data therefore show that we have engineered a site-activated agent, which only has anticoagulant activity when significant amounts of thrombin are being generated.     

Field regulation of single-molecule conductivity by a charged surface atom

Electrical transport through molecules has been much studied since it was proposed that individual molecules might behave like basic electronic devices, and intriguing single-molecule electronic effects have been demonstrated. But because transport properties are sensitive to structural variations on the atomic scale, further progress calls for detailed knowledge of how the functional properties of molecules depend on structural features. The characterization of two-terminal structures has become increasingly robust and reproducible, and for some systems detailed structural characterization of molecules on electrodes or insulators is available. Here we present scanning tunnelling microscopy observations and classical electrostatic and quantum mechanical modelling results that show that the electrostatic field emanating from a fixed point charge regulates the conductivity of nearby substrate-bound molecules. We find that the onset of molecular conduction is shifted by changing the charge state of a silicon surface atom, or by varying the spatial relationship between the molecule and that charged centre. Because the shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature.     

3-A resolution structure of a protein with histone-like properties in prokaryotes

The 3-A structure of DNA-binding protein II, which exhibits histone-like properties in bacteria, has been determined. The molecule is dimeric and appears to bind to the phosphate backbone of DNA through two symmetry-related arms. A mechanism by which the protein induces DNA supercoiling is proposed.     

RhoG activates Rac1 by direct interaction with the Dock180-binding protein Elmo

The small GTPase Rac has a central role in regulating the actin cytoskeleton during cell migration and axon guidance. Elmo has been identified as an upstream regulator of Rac1 that binds to and functionally cooperates with Dock180 (refs 2-4). Dock180 does not contain a conventional catalytic domain for guanine nucleotide exchange on Rac, but possesses a domain that directly binds to and specifically activates Rac1 (refs 5, 6). The small GTPase RhoG mediates several cellular morphological processes, such as neurite outgrowth in neuronal cells, through a signalling cascade that activates Rac1 (refs 7-12); however, the downstream target of RhoG and the mechanism by which RhoG regulates Rac1 activity remain unclear. Here we show that RhoG interacts directly with Elmo in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. We conclude that RhoG activates Rac1 through Elmo and Dock180 to control cell morphology.     

含有金属-水链的DNS镍磺酸盐的合成及晶体结构

本文利用4,4’-二硝基二苯乙烯-2,2’-二磺酸(DNS),通过常规的方法合成了一个新的含有金属-水链的磺酸镍化合物,[Ni(H2O)6](DNS)·2H2O(1),并通过元素分析、红外光谱和X-射线单晶衍射方法对化合物的结构进行了表征.结构分析表明化合物1属于三斜晶系,P1空间群;晶胞参数:a=6.802(5),b=8.541(5),c=11.830(5),α=87.595(5)°,β=75.724(5)°,γ=85.771(5)°.化合物1展示了一个由金属-水链与磺酸根阴离子通过氢键作用而形成的三维超分子结构.     

基于多窗口不同特征的蛋白质相互作用位点预测

识别蛋白质相互作用位点在蛋白质功能研究中发挥着重要作用.文章从蛋白质序列出发,提取相关特征——序列谱、序列谱+信息熵,分别形成多个滑动窗口,以此构造输入特征向量.采用"留一法"生成训练数据集和测试数据集,使用支持向量机构建6种分类器,预测测试集中的表面残基是否是蛋白质相互作用位点,得到了较好的结果,说明了实验方法的有效性和可行性.     

Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein

Insect antifreeze proteins (AFP) are much more effective than fish AFPs at depressing solution freezing points by ice-growth inhibition. AFP from the beetle Tenebrio molitor is a small protein (8.4 kDa) composed of tandem 12-residue repeats (TCTxSxxCxxAx). Here we report its 1.4-A resolution crystal structure, showing that this repetitive sequence translates into an exceptionally regular beta-helix. Not only are the 12-amino-acid loops almost identical in the backbone, but also the conserved side chains are positioned in essentially identical orientations, making this AFP perhaps the most regular protein structure yet observed. The protein has almost no hydrophobic core but is stabilized by numerous disulphide and hydrogen bonds. On the conserved side of the protein, threonine-cysteine-threonine motifs are arrayed to form a flat beta-sheet, the putative ice-binding surface. The threonine side chains have exactly the same rotameric conformation and the spacing between OH groups is a near-perfect match to the ice lattice. Together with tightly bound co-planar external water, three ranks of oxygen atoms form a two-dimensional array, mimicking an ice section.     

油船舷侧局部结构冗余度研究

为研究油船舷侧局部结构的破坏机理,建立冗余度评估方法,预报油船舷侧局部结构失效后的安全性。基于冗余技术的并行原理,在三舱段分析模型的基础上,进行油船舷侧局部结构失效路径判断,并基于后屈曲理论和非线性有限元方法,应用储备冗余度因子作为结构冗余度的表达形式,对油船舷侧局部结构冗余度进行研究。结果表明：初步得到油船舷侧局部结构的失效路径符合实际,其中舷侧横框架失效,会随即引起舷侧结构整体失效,需要引起关注;目标船的舷侧局部结构冗余度计算结果不满足要求,与本文失效路径判断结果一致。