A structural taxonomy of DNA-binding domains

The structures of several classes of DNA-binding domains reveal a variety of designs for recognizing a specific site on DNA.     

Complete protein sequence and identification of structural domains of human apolipoprotein B

Epidemiological, pathological and genetic studies show a strong positive correlation between elevated plasma concentrations of low-density lipoprotein (LDL) cholesterol and the risk of premature coronary heart disease. Apolipoprotein (apo) B-100 is the sole protein component of LDL and is the ligand responsible for the receptor-mediated uptake and clearance of LDL from the circulation. Apo B-100 is made by the liver and is essential for the assembly of triglyceride-rich very low-density lipoproteins (VLDL) in the cisternae of the endoplasmic reticulum and for their secretion into the plasma. VLDL transports triglyceride to peripheral muscle and adipose tissue, where the triglyceride is hydrolysed by lipoprotein lipase. The resultant particle, relatively enriched in cholesteryl ester, constitutes LDL. LDL delivers cholesterol to peripheral tissues where it is used for membrane and steroid hormone biosynthesis and to the liver, the only organ which can catabolize and excrete cholesterol. Plasma LDL levels are therefore determined by the balance between their rate of production from VLDL and clearance by the hepatic LDL (apo B/E) receptor pathway. Here we report the complete 4,563-amino-acid sequence of apo B-100 precursor (relative molecular mass (Mr) 514,000 (514K] determined from complementary DNA clones. Numerous lipid-binding structures are distributed throughout the extraordinary length of apo B-100 and must underlie its special functions as a nucleus for lipoprotein assembly and maintenance of plasma lipoprotein integrity. A domain enriched in basic amino-acid residues has been identified as important for the cellular uptake of cholesterol by the LDL receptor pathway.     

GLI3 zinc-finger gene interrupted by translocations in Greig syndrome families.

The Greig cephalopolysyndactyly syndrome (GCPS) is an autosomal dominant disorder affecting limb and craniofacial development in humans. GCPS-affected individuals are characterized by postaxial polysyndactyly of hands, preaxial polysyndactyly of feet, macroephaly, a broad base of the nose with mild hypertelorism and a prominent forehead. The genetic locus has been pinpointed to chromosome 7p13 by three balanced translocations associated with GCPS in different families. This assignment is corroborated by the detection of two sporadic GCPS cases carrying overlapping deletions in 7p13 (ref. 7), as well as by tight linkage of GCPS to the epidermal growth factor receptor gene in 7p12-13 (ref. 8). Of the genes that map to this region, those encoding T cell receptor-gamma, interferon-beta 2, epidermal growth factor receptor, and Hox1.4, a potential candidate gene for GCPS, have been excluded from the region in which the deletions overlap. Here we show that two of the three translocations interup the GLI3 gene, a zinc-finger gene of the GLI-Krüppel family already localized to 7p13 (refs 5, 6). The breakpoints are within the first third of the coding sequence. In the third translocation, chromosome 7 is broken at about 10 kilobases downstream of the 3' end of GLI3. Our results indicate that mutations disturbing normal GLI3 expression may have a causative role in GCPS.     

Modular arrangement of functional domains along the sequence of an aminoacyl tRNA synthetase

Gene deletions show that much of Escherichia coli alanine tRNA synthetase is dispensable for each of three activities and that these activities appear to require specific domains arranged linearly along the polypeptide. Thus, variable fusions of extra polypeptide domains to a catalytic core may account for the diverse of aminoacyl tRNA synthetases.     

拟连续domain的网式刻画

本文在定向完备偏序集上引入网的广义S收敛的概念,并给出了拟连续domain的如下网式刻画:定向完备偏序集是拟连续的当且仅当广义S收敛关于Scott拓扑是拓扑的.该结果推广了Domain理论中关于连续domain的类似刻画.     

Demonstration by NMR of folding domains in lysozyme

Although there has been much speculation on the pathways of protein folding, only recently have experimental data on the topic been available. The study of proteins under conditions where species intermediate between the fully folded and unfolded states are stable has provided important information, for example about the disulphide intermediates in BPTI, cis/trans proline isomers of RNase A3 and the molten globule state of alpha-lactalbumin. An alternative approach to investigating folding pathways has involved detection and characterization of transient conformers in refolding studies using stopped-flow methods coupled with NMR measurements of hydrogen exchange. The formation of intermediate structures has been detected in the early stages of folding of cytochrome c, RNaseA and barnase. For alpha-lactalbumin, hydrogen exchange kinetics monitored by NMR proved to be crucial for identifying native-like structural features in the stable molten globule state. An analogous partially folded protein stable under equilibrium conditions has not been observed for the structurally homologous protein hen egg-white lysozyme, although there is evidence that a similar but transient state is formed during refolding. Here we describe NMR experiments based on competition between hydrogen exchange and the refolding process which not only support the existence of such a transient species for lysozyme, but enable its structural characteristics to be defined. The results indicate that the two structural domains of lysozyme are distinct folding domains, in that they differ significantly in the extent to which compact, probably native-like, structure is present in the early stages of folding.     

如何用数列极限定义证明数列极限问题

以数列极限为例,详细阐述了用极限定义证明极限存在的三种常用的方法:基本方法、适当放大法、条件放大法,以及在应用这些方法时应注意的一些主要问题,从而强化对极限概念的理解·     

Mechanism of colour discrimination by a bacterial sensory rhodopsin

A photosensitive protein resembling the visual pigments of invertebrates enables phototactic archaebacteria to distinguish colour. This protein exists in two spectrally-distinct forms, one of which is a transient photoproduct of the other and each of which undergoes photochemical reactions controlling the cell's swimming behaviour. Activation of a single pigment molecule in the cell is sufficient to signal the flagellar motor. This signal-transduction mechanism makes evident a colour-sensing capability inherent in the retinal/protein chromophore.     

用Haar小波联合变换相关器进行模式识别

在联合变换相关器中应用Harr小波滤波器进行模式识别，并利用参考自相关谱抽取的方法来削弱零级直流发量，模拟结果表明，可以有效提高系统的抗噪声能力和鉴别率。     

底凹弹侧壁斜孔减小底阻分析

超音速条件下，弹丸的空气阻力波阻，底阻和摩阻，其中底阻约占总阻的２０％￣４０％，减小弹丸飞行中的空气阻力对改善其弹道性能是十分有利的。该文提出一个底凹弹在超声速上侧壁开孔减小底阻的数学力学模型。该模型经计算结果表明，与以往的实验结果相吻合，可作为探索凹弹侧壁开孔减阻效应和工程计算的基础。文末对侧壁斜孔的不同参数对底阻的影响作了计算分析和讨论。     

用Riesz基函数表达的多分辨分析模型

建立了用Riesz基函数表达的多分辨分析模型，在模型中研究了空间正交性条件与完全重构条件的满足，得出了包含正交小波分析的更具普遍性的多分辨分析模型。     

基于基函数的网络协议分析方法

网络协议分析可以帮助安全人员分析网络漏洞。但网络协议分析面临着协议种类越来越多、协议状态空间越来越复杂的问题。首先提出了基于基函数的网络协议结构表征方法,然后在此基础上给出了基于基函数组合模式的分层协议分析方法。之后针对私有协议,提出了一种可自学习的基函数及其组合模式扩展方式。最后给出了基于基函数的网络协议分析流程。性能分析实验表明提出的方法优于传统的匹配方法和统计方法。     

Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains

Specific sorting signals direct transmembrane proteins to the compartments of the endosomal-lysosomal system. Acidic-cluster-dileucine signals present within the cytoplasmic tails of sorting receptors, such as the cation-independent and cation-dependent mannose-6-phosphate receptors, are recognized by the GGA (Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding) proteins. The VHS (Vps27p, Hrs and STAM) domains of the GGA proteins are responsible for the highly specific recognition of these acidic-cluster-dileucine signals. Here we report the structures of the VHS domain of human GGA3 complexed with signals from both mannose-6-phosphate receptors. The signals bind in an extended conformation to helices 6 and 8 of the VHS domain. The structures highlight an Asp residue separated by two residues from a dileucine sequence as critical recognition elements. The side chains of the Asp-X-X-Leu-Leu sequence interact with subsites consisting of one electropositive and two shallow hydrophobic pockets, respectively. The rigid spatial alignment of the three binding subsites leads to high specificity.