DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

The Database of Interacting Proteins (DIP: http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein–protein interactions. It provides the scientific community with an integrated set of tools for browsing and extracting information about protein interaction networks. As of September 2001, the DIP catalogs ~11 000 unique interactions among 5900 proteins from >80 organisms; the vast majority from yeast, Helicobacter pylori and human. Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein–protein interactions available in the DIP database.     

The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins

The MiSink Plugin converts Cytoscape, an open-source bioinformatics platform for network visualization, to a graphical interface for the database of interacting proteins (DIP: http://dip.doe-mbi.ucla.edu). Seamless integration is possible by providing bi-directional communication between Cytoscape and any Web site supplying data in XML or tab-delimited format. Availability: MiSink is freely available for download at http://dip.doe-mbi.ucla.edu/Software.cgi.     

Coevolution of Interacting Fertilization Proteins

Reproductive proteins are among the fastest evolving in the proteome, often due to the consequences of positive selection, and their rapid evolution is frequently attributed to a coevolutionary process between interacting female and male proteins. Such a process could leave characteristic signatures at coevolving genes. One signature of coevolution, predicted by sexual selection theory, is an association of alleles between the two genes. Another predicted signature is a correlation of evolutionary rates during divergence due to compensatory evolution. We studied female–male coevolution in the abalone by resequencing sperm lysin and its interacting egg coat protein, VERL, in populations of two species. As predicted, we found intergenic linkage disequilibrium between lysin and VERL, despite our demonstration that they are not physically linked. This finding supports a central prediction of sexual selection using actual genotypes, that of an association between a male trait and its female preference locus. We also created a novel likelihood method to show that lysin and VERL have experienced correlated rates of evolution. These two signatures of coevolution can provide statistical rigor to hypotheses of coevolution and could be exploited for identifying coevolving proteins a priori. We also present polymorphism-based evidence for positive selection and implicate recent selective events at the specific structural regions of lysin and VERL responsible for their species-specific interaction. Finally, we observed deep subdivision between VERL alleles in one species, which matches a theoretical prediction of sexual conflict. Thus, abalone fertilization proteins illustrate how coevolution can lead to reproductive barriers and potentially drive speciation.     

The RNA Modification Database: 1999 update.

The RNA Modification Database (http://medlib.med.utah.edu/RNAmods/) provides a comprehensive listing of naturally modified nucleosides in RNA. Each file includes: chemical structure; common name and symbol; type(s) of RNA in which found and corresponding phylogenetic distribution; Chemical s registry number and index name; and initial literature citations for structure characterization and chemical synthesis. New features include capability to search database files by name or substructural features, modifications in tmRNA, and links to related data and sites.     

The Molecular Biology Database Collection: 2002 update

The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org.     

The Database of Ribosomal Cross-links: an update.

The Database of Ribosomal Cross-links (DRC) was created in 1997. Here we describe new data incorporated into this database and several new features of the DRC. The DRC is freely available via World Wide Web at http://visitweb.com/database/ or http://www. mpimg-berlin-dahlem.mpg.de/ approximately ag_ribo/ag_brimacombe/drc/     

Identification of Connexin-43 Interacting Proteins

Connexin-43 (Cx43), the most ubiquitously expressed vertebrate gap junction protein, has been shown to interact directly with Zonula Occludens-1 (ZO-1). Although several potential functions have been proposed for the ZO-1/Cx43 interaction, the role that ZO-1 and other Cx43-interacting partners play in the regulation of Cx43 trafficking, assembly, gating and turnover are not well understood. We believed a thorough analysis and classification of other Cx43-interacting proteins might help us to understand and better test these roles. We approached this question by utilizing Tandem Mass Spectrometry (MS/MS) analysis to identify proteins from normal rat kidney whole cell lysates that could interact with the C-terminal region of Cx43. Comparison against protein sequence databases identified 19 probable protein matches, including kinases, phosphatases, membrane receptors, cell signaling molecules and scaffolding proteins. We have further characterized some of these interacting proteins, including Zonula Occludens-2 (ZO-2), via western blotting and “pull down” experiments. Further in vitro/in vivoanalysis of these interacting proteins will help in our understanding of the global role of connexins in regulating development, cell metabolism and growth.     

Human Cytidine Triphosphate Synthetase 1 Interacting Proteins

We investigated the interacting proteins and intracellular localization of CTP synthetase 1 (CTPS1) in mammalian cells. CTPS1 interacted with a GST- peptidyl prolyl isomerase, Pin1 fusion (GST-Pin1) in a Ser 575 (S575) phosphorylation-dependent manner. Immunoprecipitation experiments demonstrated that CTPS1 also bound tubulin, and thirteen additional coimmunoprecipitating proteins were identified by mass spectrometry. Immunolocalization experiments showed that tubulin and CTPS1 colocalized subcellularly. Taxol treatment enhanced this but cotreatment of cells with the CTPS inhibitor, cyclopentenyl cytosine (CPEC), and taxol failed to disrupt the colocalization. Thus, these studies provide novel information on the potential interacting proteins that may regulate CTPS1 function or intracellular localization.     

Revealing of Proteins Interacting with Na,K-ATPase

Proteins interacting with 11-type of Na,K-ATPase were revealed in pig kidney outer medulla and duck salt glands using three different methods (immunoprecipitation, protein overlay, and chemical cross-linking). Immunoprecipitation was performed after solubilization of protein homogenate with Triton X-100 so that both membrane and cytosol proteins bound to Na,K-ATPase could be revealed. Two other methods were used to study the interaction of cytosol proteins with purified Na,K-ATPase. The sets of proteins revealed by each method in outer medulla of pig kidney were different. Proteins interacting with Na,K-ATPase that have molecular masses 10, 15, 70, 75, 105, 120, and 190 kD were found using the immunoprecipitation method. The chemical cross-linking method revealed proteins with molecular masses 25, 35, 40, 58, 68-70, and 86-88 kD. The protein overlay method revealed in the same tissue proteins with molecular masses 38, 42, 43, 60, 62, 66, 70, and 94 kD.     

HeLa细胞中与组织型转谷氨酰胺酶相互作用蛋白质的筛选

组织型转谷氨酰胺酶 (tissuetransglutaminase ,tTG ,TGII)是转谷氨酰胺酶家族成员之一 ,多数细胞凋亡过程中均有tTG表达水平的升高。为研究tTG在细胞凋亡过程中发挥作用的机制 ,利用Gal 4酵母双杂交系统筛选了HeLa细胞中与tTG相互作用的蛋白质 ,获得了 17个阳性酵母克隆。序列测定显示其中 1个克隆所含cDNA序列编码TIA 1相关蛋白 (TIA 1 relatedprotein ,TIAR )C端 12 9个氨基酸残基序列 ,GST下拉 (pull down)实验也证实tTG与TIAR能相互作用 ,而且这种相互作用需要Ca2 参与作用。这些结果提示tTG可能通过其Ca2 依赖的转谷氨酰胺活性对TIAR进行修饰从而影响TIAR的功能 ,可能在细胞凋亡中发挥着一定的作用。     

Proteomics Uncovers Proteins Interacting Electrostatically with Thioredoxin in Chloroplasts

The ability of thioredoxin f to form an electrostatic (non-covalent) complex, earlier found with fructose-1,6-bisphosphatase, was extended to include 27 previously unrecognized proteins functional in 11 processes of chloroplasts. The proteins were identified by combining thioredoxin f affinity chromatography with proteomic analysis using tandem mass spectrometry. The results provide evidence that an association with thioredoxin enables the interacting protein to achieve an optimal conformation, so as to facilitate: (i) the transfer of reducing equivalents from the ferredoxin/ferredoxin-thioredoxin reductase complex to a target protein; (ii) in some cases, to enable the channeling of metabolite substrates; (iii) to function as a subunit in the formation of multienzyme complexes.     

酵母双杂交技术研究与人孕酮受体B相互作用的蛋白质

应用酵母双杂交技术研究与人孕酮受体B（hPRB）发生相互作用的蛋白质,有助于进一步阐明其在乳腺癌的发生发展中发挥重要作用的调控机制。应用酵母双杂交系统3,以hPRB不同结构域为诱饵,筛选人乳腺cDNA文库,寻找能与之相互作用的蛋白质,并运用X—α—Gal等实验提供的信息,筛除假阳性克隆。最终以AF1-DBD结构域作为诱饵最终筛出了1个阳性克隆,经测序及生物信息学分析,这个克隆所编码的蛋白为PIAS3（活化的STAT3的蛋白抑制剂）。结果表明,孕激素受体可以和PIAS3发生相互作用,它们的相互作用有可能参与乳腺癌的生长调控。     

ProTherm: Thermodynamic Database for Proteins and Mutants.

The first release of the Thermodynamic Database for Proteins and Mutants (ProTherm) contains more than 3300 data of several thermodynamic parameters for wild type and mutant proteins. Each entry includes numerical data for unfolding Gibbs free energy change, enthalpy change, heat capacity change, transition temperature, activity etc., which are important for understanding the mechanism of protein stability. ProTherm also includes structural information such as secondary structure and solvent accessibility of wild type residues, and experimental methods and other conditions. A WWW interface enables users to search data based on various conditions with different sorting options for outputs. Further, ProTherm is cross-linked with NCBI PUBMED literature database, Protein Mutant Database, Enzyme Code and Protein Data Bank structural database. Moreover, all the mutation sites associated with each PDB structure are automatically mapped and can be directly viewed through 3DinSight developed in our laboratory. The database is available at the URL, http://www.rtc.riken.go.jp/protherm.htm l     

Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP)

MOTIVATION: Should reports on molecular mimicry in particular cases, e.g. responsible for cross-reactivity, be considered as accidental or as a general principle in protein evolution? To answer this question, two types of similarity have to be considered: those in homologues (synonyms) and resemblance between patches from unrelated proteins (homonyms). RESULTS: All interfaces from known protein structures were collected in a comprehensive data bank [Dictionary of Interfaces in Proteins (DIP)]. A fast, sequence-independent, three-dimensional superposition procedure was developed to search automatically for geometrically similar surface areas. Surprisingly, we found a large number of structurally similar interfaces on the surface of unrelated proteins. Even patches from different types of secondary structure were found resembling each other. The putative functional meaning of homonyms is demonstrated with striking examples.     

用亲和纯化方法筛选与gankyrin相互作用的蛋白质

目的：作为一个新发现的癌蛋白,gankyrin在肝癌细胞的发生和形成中发挥重要作用。筛选与gankyrin相互作用的蛋白质,从而进一步探讨gankyrin的作用机制。方法：采用亲和纯化技术及质谱鉴定筛选与gankyrin相互作用的蛋白质。结果：初步筛选出了6个与gankyrin发生相互作用的蛋白质,经与MSDB或NCBInr数据库比对,这6个蛋白质均是26S蛋白酶体的组成部分,其中proteasome（prosome,macropain）26S subunit,ATPase,4为已报道的蛋白质,证实结果的可靠性。结论：采用亲和纯化的方法可以有效地筛选出与gankyrin相互作用的蛋白质,为进一步研究gankyrin的作用机制及生物学功能奠定了基础。     

原癌基因LMO3相互作用蛋白的筛选及鉴定

目的 通过筛选LMO3的相互作用蛋白,进一步了解LMO3的作用及可能机制。方法酵母双杂交方法筛选LMO3相瓦作用蛋白,并通过酵母结合试验、免疫共沉淀及荧光共定位等进行验证。结果在初步获得相互作用蛋白：钙-整合素结合蛋白（Calcium—and integrin—binding protein,CIB）的基础上,在酵母中证实了LMO3与CIB的相互作用,并通过酵母结合试验确定了CIB与LMO3的相互作用位点,发现CIB可与LMO3的第一个LIM结构域（LIMI）及全长LMO3结合,免疫共沉淀试验确证了它们可以在真核细胞内结合,荧光共定位表明与CIB的相互作用可使LMO3在C8细胞中的定位由细胞核移到细胞质。结论LMO3可以与CIB在真核细胞中发生相互作用,提示LMO3可能通过与CIB的相互作用参与细胞相关功能的调节。     

Proteins of Rapid Axonal Transport: Polypeptides Interacting with the Lectin from Lens Culinavis

Abstract: Rapidly transported fucose-labelled glycoproteins from axons of rabbit retinal ganglion cells were solubilized with nonionic detergents. The labelled glycoproteins carried hydrophobic sites as revealed by a reversible binding to a hydrophobic matrix. A major portion of the labelled glycoproteins carried α-D-mannopyranoside (or glucopyranoside) residues, as shown by a specific interaction with the lectin from Lens culinaris. Three major groups of labelled polypeptides capable of binding to the lectin are described.     

应用蛋白组方法筛选血浆中乙肝病毒PreS1结合蛋白

目的筛选血浆中乙型肝炎病毒PreS1结合蛋白。方法表达纯化了PreS1-谷胱甘肽-S-转移酶（glutathione—S-transferase,GST）融合蛋白,利用该蛋白与血浆进行Pull—down实验,并设立GST与血浆Pull—down,GST、PreS1-GST与PBS Pull—down对照,Pull-down产物进行双向电泳分离（2-DE）,差异蛋白点通过质谱鉴定。结果成功表达纯化出PreS1-GST融合蛋白,通过双向电泳分析发现一个PreS1特异结合蛋白,经质谱鉴定为含锚蛋白重复序列的蛋白57（ANKRD57）。结论锚蛋白重复序列的主要功能是介导蛋白质与蛋白质之间的相互作用,ANKRD57与PreS1特异结合后的生理功能值得深入研究。