Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function

The increase in known three-dimensional protein structures enables us to build statistical profiles of important functional sites in protein molecules. These profiles can then be used to recognize sites in large-scale automated annotations of new protein structures. We report an improved FEATURE system which recognizes functional sites in protein structures. FEATURE defines multi-level physico-chemical properties and recognizes sites based on the spatial distribution of these properties in the sites' microenvironments. It uses a Bayesian scoring function to compare a query region with the statistical profile built from known examples of sites and control nonsites. We have previously shown that FEATURE can accurately recognize calcium-binding sites and have reported interesting results scanning for calcium-binding sites in the entire Protein Data Bank. Here we report the ability of the improved FEATURE to characterize and recognize geometrically complex and asymmetric sites such as ATP-binding sites and disulfide bond-forming sites. FEATURE does not rely on conserved residues or conserved residue geometry of the sites. We also demonstrate that, in the absence of a statistical profile of the sites, FEATURE can use an artificially constructed profile based on a priori knowledge to recognize the sites in new structures, using redoxin active sites as an example.     

分支位点在真核基因受体位点识别中的作用

真核基因受体位点识别是剪接位点识别的一部分,也是基因识别中的重要环节,一直受到研究人员的关注。已有的研究结果显示受体位点的识别与分支位点有关,然而关于分支位点和受体位点识别的关系问题,目前还无人将其作为专门的问题予以深入研究。从受体位点识别出发,选取不同的受体位点序列长度,以神经网络为识别工具,对分支位点在受体位点识别中的作用做了深入研究和分析。实验结果表明,受体位点序列的特征信息集中在分支位点一例,因此分支位点在受体位点识别中具有重要作用。研究结果为受体位点识别问题中序列特征提取提供了依据。     

Differential reactivity of 9-NH2-ellipticine on apurinic and apyrimidinic sites in circular DNA

Endonucleases for apurinic sites as well as chemical compounds reacting with aldehydes do not generally differentiate between apurinic and apyrimidinic sites. We have studied the effect of the apurinic site reagent, 9-NH2-ellipticine, on apyrimidinic sites enzymatically generated on PBR322 DNA and compared it to its' action on apurinic PM2 and PBR322 DNAs. In conditions where this compound induces breakage of apurinic sites, it does not display any action on apyrimidinic sites.     

Heritable fragile sites on human chromosomes II. Distribution, phenotypic effects, and cytogenetics.

Individuals and families have been documented in which there are a number of fragile sites on chromosomes. These include sites at 2q11, 10q23, 11q13, 16p124, 16q22, 20p11, and Xq27 or 28. Fragile sites reported in the literature are compiled. The cytogenetics of the sites is discussed. The phenotypic effects of the sites are considered, and it is speculated that homozygosity of the autosomal sites might be deleterious as is hemizygosity of the site on Xq. These sites are used in the previous report which documents the effect of tissue medium components on their expression.     

Detection of IgA-binding sites on human immunodeficiency virus type-1 envelope glycoproteins, Gp120 and Gp41

IgA has been supposed to play an important role in the prevention of HIV-1 infection. In this study, IgA-binding sites on gp120 and gp41 of HIV-1 envelope glycoproteins were analyzed using ELISA and overlapping synthetic peptides covering all of the gp120 and gp41 sites. IgA antibodies in plasma and saliva mainly bound to six and five sites on gp120 and gp41, respectively. Some of the IgA-binding sites differed from those of IgG-binding sites and the amount of IgA antibodies that bound to each site varied among samples. IgA antibodies in some plasma samples neutralized HIV-1 infection, and those IgA antibodies contained the antibodies which bound to the V3, C3 and ELDKWA sites. The results suggest that IgA antibodies which bind to certain sites on HIV-1 envelope glycoproteins may neutralize HIV-1 infection, presumably at mucosal sites where most IgA antibodies are produced. The induction of IgA antibodies that bind specific sites and neutralize HIV-1 infection at mucosal sites may be important in the development of a vaccine against HIV-1 infection.     

西藏红拉雪山滇金丝猴的夜宿地与夜宿树选择

树栖灵长类动物要在夜宿地度过半生以上的时光,因此选择合适的夜宿地及夜宿树对其存活尤为关键。影响夜宿地以及夜宿树选择的主要因素是逃避天敌捕食,但对于栖息在温带森林的灵长类而言,还必须面对低 温以及食物缺乏等因素的影响。2003 年6 月至2005 年3 月,采用跟踪猴群,记录夜宿地并依据地面粪便颗粒数确定夜宿树,在西藏红拉雪山自然保护区对小昌都滇金丝猴的夜宿地及夜宿树进行了研究。结果表明:在主要 研究时间段196 d 夜宿地记录中猴群使用了101 个夜宿地,使用2 次以上的夜宿地有67 个,夜宿162 d。夜宿地全部位于针叶林中,冬季夜宿地主要分布在向阳、背风和低海拔处。比较重复利用夜宿次数多与夜宿次数少的树发现:夜宿多的树高大,底枝长,而与底枝高没有差异。比较夜宿和不过夜的树发现:夜宿树高大、底枝长。这些特点表明小昌都猴群夜宿地及夜宿树的选择可能受到逃避天敌和体温调节的影响。     

Basolateral distribution of fibronectin matrix assembly sites on vascular endothelial monolayers is regulated by substratum fibronectin.

Endothelial cells exhibit binding sites for the amino terminus of fibronectin that participate in subendothelial fibronectin matrix assembly. These binding sites, termed matrix assembly sites, are localized on the basolateral surface of confluent endothelial monolayers (Kowalczyk et al. Blood, 75:2335, 1990). The present study investigates the role of cell-cell and cell-substratum interactions in the localization of matrix assembly sites to the basal surface of endothelial cells. Cells were cultured in Transwell culture inserts and matrix assembly sites were detected by binding assays using an iodinated 70 Kd amino-terminal fibronectin fragment. Integrity of intercellular junctions was monitored by measuring protein flux across Transwell filters. Time course experiments demonstrated that matrix assembly site expression on the basolateral cell surface preceded intercellular junction formation. Transfer of confluent monolayers to calcium-free medium resulted in the loss of junctions and in an increase in 125I-70 kD binding from the apical medium. The increased 125I-70 kD binding resulted from increased access of 125I-70 kD to basolateral matrix assembly sites and not from the relocation of binding sites to the apical membrane. To determine the effect of matrix composition on matrix assembly site expression and localization, cells were seeded onto vitronectin- or fibronectin-coated substrates. Fibronectin increased the expression of matrix assembly sites on the apical surface within 24 hours. By 48 hours, matrix assembly sites were located only on the basolateral surface. Vitronectin had no effect on the expression or localization of matrix assembly sites. These results indicate that the expression and localization of matrix assembly sites on the surface of vascular endothelial cells can be regulated by substratum fibronectin.     

Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease.

The SfiI endonuclease differs from other type II restriction enzymes by cleaving DNA concertedly at two copies of its recognition site, its optimal activity being with two sites on the same DNA molecule. The nature of this communication event between distant DNA sites was analysed on plasmids with recognition sites for SfiI interspersed with recombination sites for resolvase. These were converted by resolvase to catenanes carrying one SfiI site on each ring. The catenanes were cleaved by SfiI almost as readily as a single ring with two sites, in contrast to the slow reactions on DNA rings with one SfiI site. Interactions between SfiI sites on the same DNA therefore cannot follow the DNA contour and, instead, must stem from their physical proximity. In buffer lacking Mg2+, where SfiI is inactive while resolvase is active, the addition of SfiI to a plasmid with target sites for both proteins blocked recombination by resolvase, due to the restriction enzyme bridging its sites and thus isolating the sites for resolvase into separate loops. The extent of DNA looping by SfiI matched its extent of DNA cleavage in the presence of Mg2+.     

Gin-mediated recombination of catenated and knotted DNA substrates: implications for the mechanism of interaction between cis-acting sites

The Gin DNA-inversion system of bacteriophage Mu normally requires a substrate containing two inverted recombination sites (gix) and an enhancer sequence on the same supercoiled DNA molecule. The reaction mechanism was investigated by separating these sites on catenated rings. Catenanes with the gix sites on one circle and the enhancer on the other recombined efficiently. Thus, the enhancer was fully functional even though it was located in trans to the gix sites. Multiple links between the rings are required for recombination. Multiply linked catenanes with gix sites on separate circles, one of which contained the enhancer, were also efficient substrates. Knotted constructs carrying directly repeated gix sites were recombined. Catenated and knotted substrates must also be supercoiled. These experiments eliminate simple tracking or looping models as explanations for why the enhancer and gix sites must be in cis with standard substrates. Rather, the Gin synaptic complex requires the three sites to be mutually intertwined in a right-handed fashion with a unique polarity of the gix sites. This geometry is achieved by branching of the DNA substrate and requires the energy and structure of supercoiling, catenation, or knotting.     

基于大型底栖动物群落的上海市河道水质生物学评价

2011年夏秋季,在上海市全境83个河道断面开展了河道底栖动物采样,共获取底栖动物20个分类单位（种）。9个极严重污染断面未采集到活体生物,生境基本丧失。其余74个有活体生物断面,采用三种常用生物指数：Shannon-Wiener多样性指数、Hilsenhoff耐污指数、Goodnight修正指数分别进行计算及评价。Shannon-Wiener多样性指数判别为25个严重污染和49个重污染断面;Hilsenhoff耐污指数划分38个重污染、5个中污染和31个轻污染断面;Goodnight修正指数划分33个重污染、2个中污染和39个轻污染断面。与典型河道断面的水质理化指标监测值进行对照,Shannon-Weiner多样性指数对河道水质评价的准确度较低,Hilsenhoff生物指数和Goodnight修正指数的水质评价效率及准确度均较高,断面污染等级与水质理化指标基本对应。     

A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles

Post-translational modification of proteins by ubiquitin is a fundamentally important regulatory mechanism. However, proteome-wide analysis of endogenous ubiquitylation remains a challenging task, and almost always has relied on cells expressing affinity tagged ubiquitin. Here we combine single-step immunoenrichment of ubiquitylated peptides with peptide fractionation and high-resolution mass spectrometry to investigate endogenous ubiquitylation sites. We precisely map 11,054 endogenous putative ubiquitylation sites (diglycine-modified lysines) on 4,273 human proteins. The presented data set covers 67% of the known ubiquitylation sites and contains 10,254 novel sites on proteins with diverse cellular functions including cell signaling, receptor endocytosis, DNA replication, DNA damage repair, and cell cycle progression. Our method enables site-specific quantification of ubiquitylation in response to cellular perturbations and is applicable to any cell type or tissue. Global quantification of ubiquitylation in cells treated with the proteasome inhibitor MG-132 discovers sites that are involved in proteasomal degradation, and suggests a nonproteasomal function for almost half of all sites. Surprisingly, ubiquitylation of about 15% of sites decreased more than twofold within four hours of MG-132 treatment, showing that inhibition of proteasomal function can dramatically reduce ubiquitylation on many sites with non-proteasomal functions. Comparison of ubiquitylation sites with acetylation sites reveals an extensive overlap between the lysine residues targeted by these two modifications. However, the crosstalk between these two post-translational modifications is significantly less frequent on sites that show increased ubiquitylation upon proteasome inhibition. Taken together, we report the largest site-specific ubiquitylation dataset in human cells, and for the first time demonstrate proteome-wide, site-specific quantification of endogenous putative ubiquitylation sites.     

The Atlas of Chinese World Wide Web Ecosystem Shaped by the Collective Attention Flows

The web can be regarded as an ecosystem of digital resources connected and shaped by collective successive behaviors of users. Knowing how people allocate limited attention on different resources is of great importance. To answer this, we embed the most popular Chinese web sites into a high dimensional Euclidean space based on the open flow network model of a large number of Chinese users’ collective attention flows, which both considers the connection topology of hyperlinks between the sites and the collective behaviors of the users. With these tools, we rank the web sites and compare their centralities based on flow distances with other metrics. We also study the patterns of attention flow allocation, and find that a large number of web sites concentrate on the central area of the embedding space, and only a small fraction of web sites disperse in the periphery. The entire embedding space can be separated into 3 regions(core, interim, and periphery). The sites in the core (1%) occupy a majority of the attention flows (40%), and the sites (34%) in the interim attract 40%, whereas other sites (65%) only take 20% flows. What’s more, we clustered the web sites into 4 groups according to their positions in the space, and found that similar web sites in contents and topics are grouped together. In short, by incorporating the open flow network model, we can clearly see how collective attention allocates and flows on different web sites, and how web sites connected each other.     

DNA supercoiling enables the type IIS restriction enzyme BspMI to recognise the relative orientation of two DNA sequences

Many proteins can sense the relative orientations of two sequences at distant locations in DNA: some require sites in inverted (head-to-head) orientation, others in repeat (head-to-tail) orientation. Like many restriction enzymes, the BspMI endonuclease binds two copies of its target site before cleaving DNA. Its target is an asymmetric sequence so two sites in repeat orientation differ from sites in inverted orientation. When tested against supercoiled plasmids with two sites 700 bp apart in either repeated or inverted orientations, BspMI had a higher affinity for the plasmid with repeated sites than the plasmid with inverted sites. In contrast, on linear DNA or on supercoiled DNA with sites 1605 bp apart, BspMI interacted equally with repeated or inverted sites. The ability of BspMI to detect the relative orientation of two DNA sequences thus depends on both the topology and the length of the intervening DNA. Supercoiling may restrain the juxtaposition of sites 700 bp apart to a particular alignment across the superhelical axis, but the juxtaposition of sites in linear DNA or far apart in supercoiled DNA may occur without restraint. BspMI can therefore act as a sensor of the conformational dynamics of supercoiled DNA.     

The distribution and mobility of anionic sites on the surfaces of baby hamster kidney cells

The distribution and mobility of anionic sites on the surfaces of baby hamster kidney cells were studied by utilizing the multivalent ligand, polycationic ferritin, as a visual probe. Our observations revealed that anionic sites are distributed over the entire cell surface, with the highest density of sites being located on cell surface microextensions. Following the initial binding of polycationic ferritin to the surface of unfixed cells, the ligand-bound anionic sites redistributed by migrating from the surface of microextensions to the surface of the cell body. In 20 min, this migration resulted in a total clearing of anionic sites from the surface of microextensions concomitant with the formation of patches of anionic sites on the surface of the cell body. Polycationic ferritin-induced migration and patch formation of anionic sites was not prevented by 2,4- dinitrophenol, N-ethylmaleimide, colchicine, or cytochalasin B. However, the ligand-induced redistribution of cell surface anionic sites was prevented by prefixation of cells with glutaraldehyde.     

Photosynthesis and the Web: 2001

First, a brief history of the Internet and the World Wide Web is presented. This is followed by relevant information on photosynthesis-related web sites grouped into several categories: (1) large group sites, (2) comprehensive overview sites, (3) specific subject sites, (4) individual researcher sites, (5) kindergarten through high school (K-12) educational sites, (6) books and journals, and, 7) other useful sites. A section on searching the Web is also included. Finally, we have included an appendix with all of the web sites discussed herein as well as other web sites that space did not allow. Readers are requested to send comments, corrections and additions to gov@uiuc.edu. This revised version was published online in June 2006 with corrections to the Cover Date.     

Female spawning migrations of the protogynous wrasse,Halichoeres marginatus

Spawning sites and spawning migration paths of tagged females of the protogynous wrasse,Halichoeres marginatus, were studied on the shallow reefs at Kuchierabu-jima Island, Japan. Males set up mating territories above prominent rocks on the offshore reef slope in the late afternoon, and pair-spawned with females, which had migrated there from their home ranges located in inshore areas. Small females migrated to the spawning sites near their home ranges, whereas large females migrated to various spawning sites located within a wide area, including downcurrent sites. Spawning at the downcurrent sites favors transport of eggs offshore, thereby increasing the female’s fitness. The spawning sites where an individual had spawned as a female were subsequently used for mating after it had changed sex. It is suggested that the wide migration of females to various spawning sites, enables the storing up of information on those sites, which later helps in the acquisition of mating territories after changing sex.     

Pressure pain sensitivity and hardness along human normal and sensitized muscle

The spatial distribution of pressure sensitivity and muscle hardness was examined on normal muscle tissue and muscle tissue after induction of delayed onset muscle soreness (DOMS). The pressure sensitivity and muscle hardness were assessed at nine sites on the tibialis muscle from the proximal to distal tendon on two separate days. In total 37 healthy volunteers participated in three experiments. In the first experiment pressure pain threshold (PPT) and pressure pain tolerance (PPTO) were assessed. Decreased PPT and PPTO were found on day 2, 7 days after day 1. Proximal and distal stimulation sites were harder compared to muscle belly sites. In a second experiment two different probe sizes were used. Variation in PPT between the nine sites was found for the large probe with muscle belly being less sensitive to pressure stimulation compared to proximal and distal sites. The most proximal stimulation site was harder compared to muscle belly sites. In a third experiment PPT and muscle hardness were assessed before and 48?h after eccentric exercise. PPT at two muscle belly sites was significantly decreased during DOMS. No specific sites were harder during DOMS, the average muscle hardness across sites was however significantly increased. Decreased PPT and increased muscle hardness did not correlate. In conclusion, within subjects the pressure sensitivity varies along the musculoskeletal unit. In DOMS, specific muscle belly sites were more sensitive to pressure stimulation. Muscle–tendon sites were harder compared to muscle belly sites.