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At least 721 records · Page 40Linked to original sources

PubMed2001

Thermodynamic database for protein-nucleic acid interactions (ProNIT).

MOTIVATION: Protein-nucleic acid interactions are fundamental to the regulation of gene expression. In order to elucidate the molecular mechanism of protein-nucleic acid recognition and analyze the gene regulation network, not only structural data but also quantitative binding data are necessary. Although there are structural databases for proteins and nucleic acids, there exists no database for their experimental binding data. Thus, we have developed a Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT). RESULTS: We have collected experimentally observed binding data from the literature. ProNIT contains several important thermodynamic data for protein-nucleic acid binding, such as dissociation constant (K(d)), association constant (K(a)), Gibbs free energy change (DeltaG), enthalpy change (DeltaH), heat capacity change (DeltaC(p)), experimental conditions, structural information of proteins, nucleic acids and the complex, and literature information. These data are integrated into a relational database system together with structural and functional information to provide flexible searching facilities by using combinations of various terms and parameters. A www interface allows users to search for data based on various conditions, with different display and sorting options, and to visualize molecular structures and their interactions. AVAILABILITY: ProNIT is freely accessible at the URL http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html.

Amino Acid Sequence↗

PubMed2006

Mass spectrometric characterization of low-molecular-mass color pI markers and their use for direct determination of pI value of proteins.

The use of low-molecular-mass color pI markers for the determination of pI values of proteins in gel isoelectric focusing (IEF) in combination with mass spectrometry is described. Different types of substituted phenols of known pI values within the mass range 250-400 were used here as pI markers. The pure, synthesized pI markers were studied by MALDI-TOF/TOF MS. Fragmentation studies of the pI markers were also performed. Only stable and well-characterized pI markers were used in this work. The selected pI markers were mixed with proteins, deposited on a gel and separated in a pH gradient. Color pI markers enable supervision of progress of the focusing process and also estimation of the position of the invisible focused bands. The separated bands of the pI markers (containing separated proteins) were excised, and the pI markers were eluted from each gel piece by water/ethanol and identified by MALDI-TOF/TOF MS. From the washed gel pieces the remaining carrier ampholytes were then washed out and proteins were in-gel digested with trypsin. The obtained peptides were measured by MALDI-TOF/TOF MS and the proteins identified via a protein database search. This procedure allows avoiding time-consuming protein staining and destaining procedures, which shortens the analysis time roughly by half. For comparison, IEF gels were stained with Coomassie Brilliant Blue R 250 and proteins in the gel bands were identified according to the standard proteomic protocol. This work has confirmed that our approach can give information about the correct pI values of particular proteins and shorten significantly the time of analysis.

Color↗

PubMed2000

yam8(+), a Schizosaccharomyces pombe gene, is a potential homologue of the Saccharomyces cerevisiae MID1 gene encoding a stretch-activated Ca(2+)-permeable channel.

The Saccharomyces cerevisiae MID1 gene encodes a stretch-activated Ca(2+)-permeable channel. In a protein database, we found a Schizosaccharomyces pombe gene whose predicted protein shows 26% identical and 62% similar to the Mid1 channel in amino acid sequence. cDNA derived from this gene, designated yam8(+), was isolated by reverse transcription-polymerase chain reaction (RT-PCR). Further analysis showed that the Yam8 protein consists of 486 amino acids and has 6 hydrophobic segments. The yam8(+) cDNA, placed under the S. cerevisiae TDH3 promoter, partially complemented the mating pheromone-induced death (mid) phenotype of the S. cerevisiae mid1 mutant. The expression of the yam8(+) cDNA in the mid1 mutant cells partially remediated the mid phenotype and resulted in a slight increase in Ca(2+) uptake activity. These findings suggest that Yam8 is a potential homologue of Mid1.

Amino Acid Sequence↗

PubMed2006

Proteome comparison following self- and across-pollination in self-incompatible apricot (Prunus armeniaca L.).

The study compared the protein differences between self- and across-pollinated self-incompatible (SI) apricots by two-dimensional gel electrophoresis and liquid chromatography-electrospray ion trap tandem mass spectrometry, the results showed that nine protein spots were expressed in self-pollinated pistil and only one was expressed in cross-pollinated pistils. Sixteen and three protein spots were up- and down-regulated in cross-pollinated pistils, respectively, compared with self-pollinated pistils. Seven protein spots were identified unambiguously by SEQUEST in NCBI protein database: Actin-12, enolase, MYB transcription-factor-like protein, heat-shock protein 70 were upregulated in cross-pollinated pistils compared with self-pollinated pistils; and actin-7, actin-8 and fructose bisphosphate aldolase-like protein were detected only in self-pollinated pistils.

Amino Acid Sequence↗

PubMed1990

Identification of a group of proteins that are strongly up-regulated in total epidermal keratinocytes from psoriatic skin.

Analysis using two-dimensional (2D) gel electrophoresis of the [35S]-methionine-labelled proteins synthesized by non-cultured total epidermal keratinocytes obtained from normal and psoriatic skin revealed 6 proteins that are strongly up-regulated (5 times or more) in psoriatic skin. These proteins are synthesized at albeit lower levels by keratinocytes from normal and normal-appearing (uninvolved) skin of psoriatic patients, and correspond to isoelectric focusing sample spot numbers 4311 (40.3 kDa), 4003 (12.4 kDa), 5008 (11.9 kDa), 3012 (11.6 kDa), 6016 (11.6 kDa) and 1015 (10.1 kDa) in the normal keratinocyte 2D gel protein database [Celis et al, (1990) Electrophoresis, in press]. These proteins are also detected in the labelling medium indicating that they are at least in part secreted. Given their striking regulatory behavior, these proteins may play a role in the pathogenesis of psoriasis.

Electrophoresis, Gel, Two-Dimensional↗

PubMed1992

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids.

A new interactive graphics program is described that provides a quick and simple procedure for identifying, displaying, and manipulating the indentations, cavities, or holes in a known protein structure. These regions are defined as, e.g., the xo, yo, zo values at which a test sphere of radius r can be placed without touching the centers of any protein atoms, subject to the condition that there is some x < xo and some x > xo where the sphere does touch the protein atoms. The surfaces of these pockets are modeled using a modification of the marching cubes algorithm. This modification provides identification of each closed surface so that by "clicking" on any line of the surface, the entire surface can be selected. The surface can be displayed either as a line grid or as a solid surface. After the desired "pocket" has been selected, the amino acid residues and atoms that surround this pocket can be selected and displayed. The protein database that is input can have more than one protein "segment," allowing identification of the pockets at the interface between proteins. The use of the program is illustrated with several specific examples. The program is written in C and requires Silicon Graphics graphics routines.

Algorithms↗

PubMed1993

Polar zippers.

BACKGROUND: Certain proteins are known to form leucine zippers - alpha-helical coiled-coils in which the non-polar side chains of two leucine-rich helices intermesh. We recently presented the first evidence for a polar zipper, formed by the carboxy-terminal peptides of the eight subunits of Ascaris haemoglobin. The evidence was based on the presence of pairs of acidic residues alternating with pairs of basic residues ( + + - - ) in an amino-acid sequence that has since been shown to be incomplete. The complete sequence, derived from the haemoglobin's cDNA, now shows a self-complementary polar sequence extending along the entire length of its 24-residue carboxy-terminal peptide. RESULTS: From the complete sequence, it is clear that the eight identical subunits of the haemoglobin could be held together by an eight-stranded antiparallel beta barrel made up of the carboxy-terminal 24 residues of each of the subunits, such that each strand forms 10 salt bridges with each of its neighbours. A computer search of the protein database revealed similar, but shorter, + + - - repeats in several other proteins. It also revealed long repeats of alternating arginine and aspartate residues, and long stretches of only glutamines, or only serines, suggestive of several other kinds of polar zippers. CONCLUSION: Several proteins have amino-acid sequences that suggest the formation of polar zippers made of beta strands. These could form antiparallel pleated sheets linked together by hydrogen bonds between polar side chains both above and below the plane of the sheets. Polar zippers may be important in welding together oligomeric proteins which have subunits lacking the extensive complementary surfaces necessary for stability, or in promoting the association of functionally complementary proteins.

Journal Article↗

PubMed2005

Clast4, the murine homologue of human eIF4E-Transporter, is highly expressed in developing oocytes and post-translationally modified at meiotic maturation.

In metazoans, translational regulation of a set of maternal mRNAs directs oocyte maturation and early embryogenesis. These transcripts are often kept dormant until their products are spatially and temporally required in development. The interaction between general translation factors (i.e. eIF4E) and their specific interactors influences translation initiation. A search of the protein database for a mouse homologue of the Drosophila Cup protein, a translational repressor during female germ-line development, identified the product of the Clast4 gene. In this report, we show that Clast4 mRNA and protein are highly expressed within the cytoplasm of growing oocytes. The Clast4 protein is stable during this developmental window and post-translationally modified by phosphorylation upon oocyte meiotic maturation. Additionally, we show that Clast4 and eIF4E directly interact by means of a canonical and functional eIF4E-binding motif. Our results suggest that Clast4, similar to Drosophila Cup, may act at the translational level during murine female germ-line development.

3' Untranslated Regions↗

PubMed1997

Characterization and identification of latex allergens by two-dimensional electrophoresis and protein microsequencing.

BACKGROUND: Proteins of natural rubber latex cause IgE-mediated sensitization in 3% to 18% of health care workers and in up to 50% of patients with spina bifida. OBJECTIVE: This study was aimed at the generation of a comprehensive latex protein database by two-dimensional electrophoresis (2-DE). METHODS: Proteins extracted from fresh Hevea brasiliensis latex were separated by 2-DE. IgE-reactive proteins were analyzed by immunoblotting with sera of health care workers with latex allergy. Protein microsequencing and monoclonal antibodies were used to identify the latex allergens. RESULTS: The latex C-serum 2-DE map was very complex and exhibited about 200 distinct polypeptides. The proteins eluted from the latex particles consisted primarily of two groups of acidic proteins located in the 8 to 14 kd and 22 to 24 kd areas of the 2-DE map. Major IgE-reactivity was detected with C-serum proteins in the 56, 45, 30, 20, 14, and <6.5 kd areas of the immunoblots. The 8 to 14 kd particle proteins exhibited distinct IgE reactivity, whereas the 22 to 24 kd proteins were not stained. Seven of the soluble IgE-reactive protein spots showed high homology with enolase, superoxide dismutase, triosephosphate isomerase, proteasome subunit, and chitinase and represent previously undescribed latex allergens; whereas nine protein spots corresponded to known latex allergens, namely prohevein, hevein, prohevein C-domain, and hevamine. As identified by monoclonal antibodies, the IgE-reactive latex particle proteins mainly represent the allergenic rubber elongation factor. CONCLUSIONS: Two-dimensional electrophoresis, followed by immunoblotting and protein microsequencing, can rapidly identify a large number of IgE-binding latex proteins. The 2-DE latex maps generated will provide valuable information for the development of strategies to isolate the relevant latex allergens. Because the novel latex allergens are common plant enzymes, they may also act as cross-reacting proteins in various foods.

Adult↗

PubMed1997

New genes for male accessory gland proteins in Drosophila melanogaster.

The accessory gland of male insects produces components of the seminal fluid that alter the behavior, physiology and life span of the mated female, and contribute to her efficient storage and utilization of sperm. As a step towards understanding how this occurs, we have isolated genes encoding 12 previously unreported accessory gland-specific mRNAs from the fruit fly Drosophila melanogaster. We report here the restriction maps of the new genes, the chromosome positions--which are all autosomal--of the 11 non-repetitive genes, their expression patterns, and the sequences of the accessory gland proteins (Acps) encoded by nine of the genes. Eight of the proteins predicted from these sequences begin with putative secretion signals. Following their signal sequences, three of the predicted molecules are peptides and the other five are larger polypeptides with characteristics of cleavable prohormones. The ninth molecule, which has an N-terminal hydrophobic region but no consensus signal peptide cleavage site, is predicted to be a 716 amino acid glycoprotein. Of the nine proteins, two have intriguing similarities to sequences in protein databases. Acp76A is a 388 amino acid pro-protein which contains a signature sequence for the serpin class of protease inhibitors. The 115 amino acid Acp62F has a 28 amino acid region of high sequence similarity to a neurotoxin of the Brazilian armed spider Phoneutria nigriventer. Models are discussed in which Acp76A plays a role in the observed regulation of Acp proteolysis and/or in the coagulation of seminal fluid to form a mating plug, and in which Acp62F contributes to the reported toxicity of Drosophila seminal fluid.

Animals↗

PubMed2001

Cloning and characterization of leaf senescence up-regulated genes in sweet potato.

Genes that are expressed during leaf senescence in sweet potato (Ipomoea batatas, cv. Tainong 57) were identified by the isolation of cDNA fragments with the mRNA differential display method. Eight senescence-associated cDNA clones for mRNAs differentially expressed during leaf senescence were obtained and characterized. Northern blot analysis indicated that all these clones represented genes that are up-regulated during natural leaf senescence. Among them, five cDNA clones have been obtained in full length by screening a senescing leaf cDNA library or by performing rapid amplification of cDNA ends. DNA and protein database searches revealed that clones SPA15 and SPC9 encode proteins of unknown function. The other six clones SPG31, SPC20, SPG27, SPC25, SPC15 and SPC1 showed significant sequence homology to known genes encoding a cysteine proteinase, isocitrate lyase, S-adenosylmethionine decarboxylase, cysteine proteinase inhibitor and metallothionein-like type I protein. The gene expression patterns represented by SPG31, SPG27 and SPA15 were found to be highly specific in senescing leaves. The corresponding transcripts for SPG31, SPG27 and SPA15 were below detectable levels in other organs such as flowers, stems, roots and tubers. The possible physiological roles of these gene products in the leaf senescence process are discussed.

Journal Article↗

PubMed2002

Conventional and functional proteomics using large format two-dimensional gel electrophoresis 24 hours after controlled cortical impact in postnatal day 17 rats.

Conventional and functional proteomics have significant potential to expand our understanding of traumatic brain injury (TBI) but have not yet been used. The purpose of the present study was to examine global hippocampal protein changes in postnatal day (PND) 17 immature rats 24 h after moderate controlled cortical impact (CCI). Silver nitrate stains or protein kinase B (PKB) phosphoprotein substrate antibodies were used to evaluate high abundance or PKB pathway signal transduction proteins representing conventional and functional proteomic approaches, respectively. Isoelectric focusing was performed over a nonlinear pH range of 3-10 with immobilized pH gradients (IPG strips) using supernatant from the most soluble cellular protein fraction of hippocampal tissue protein lysates from six paired sham and injured PND 17 rats. Approximately 1,500 proteins were found in each silver stained gel with 40% matching of proteins. Of these 600 proteins, 52% showed a twofold, 20% a fivefold, and 10% a 10-fold decrease or increase. Spot matching with existing protein databases revealed changes in important cytoskeletal and cell signalling proteins. PKB substrate protein phosphorylation was best seen in large format two-dimensional blots and known substrates of PKB such as glucose transporter proteins 3 and 4 and forkhead transcription factors, identified based upon molecular mass and charge, showed altered phosphorylation 24 h after injury. These results suggest that combined conventional and functional proteomic approaches are powerful, complementary and synergistic tools revealing multiple protein changes and posttranslational protein modifications that allow for more specific and comprehensive functional assessments after pediatric TBI.

Age Factors↗

PubMed2000

Two novel transcripts expressed in pea dormant axillary buds.

To elucidate the molecular mechanism of apical dominance, the expression patterns of genes that are preferentially expressed in dormant axillary buds of pea (Pisum sativum L. cv. Alaska) seedlings were investigated. We isolated two cDNA clones, cPsAD1 and cPsAD2 whose corresponding genes were named PsAD1 and PsAD2, from a cDNA library of dormant axillary buds using the differential display method. The deduced amino acid sequence of PsAD1 contains 87 residues and is rich in glycine residues in the amino terminal region. A search of the protein databases failed to find any sequences similar to PsAD1 protein except for the glycine-rich region. Northern blot analyses showed that PsAD1 mRNA mainly accumulated in dormant axillary buds and that its amount rapidly decreased after decapitation of the terminal bud. In situ hybridization analyses indicated that PsAD1 mRNA was localized in the apical meristem, procambia, and leaf primordia in dormant axillary buds that were competent to grow out but whose growth was temporarily suspended. That is, the expression of the PsAD1 gene is closely associated with the dormancy of axillary buds. The deduced amino acid sequence of PsAD2 contains 98 amino acid residues and is not similar to those of previously characterized proteins. PsAD2 mRNA accumulated in dormant axillary buds, roots, mature leaflets and elongated stems, suggesting that PsAD2 is involved in not only the dormancy of axillary buds but also the non-growing state in various tissues.

Amino Acid Sequence↗

PubMed2005

[Comparative proteomics research on removing of large invasive plasmid pINV of Shigella flexneri 2a strain 2457T].

S. flexneri 2a strain 2457T and its derivative without large invasive plasmid pINV-2457T were cultured to middle logarithm phase. Whole cellular protein extracts of the two strains were examined by two dimensional (2D) electrophoresis using immobilized pH gradient (IPG) technology. After in-gel protein digestion, the different-expressed spots were detected by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS). All the peptide mass fingerprints (PMFs) were searched by the program Mascot developed by Matrix Science Ltd. For identifying proteins, databases of S. flexneri 2a 2457T was used. Ten proteins with changed expression level were found. Results indicate that expression levels of several enzymes involved in nucleic acid metabolism have risen, and expression increase of deoxycytidine deaminase, purine nucleoside phosphorylase, and uridine nucleoside phosphorylase might lead to increase of uridine and uridine nucleoside synthesization.

Bacterial Proteins↗

PubMed2005

PhosphaBase: an ontology-driven database resource for protein phosphatases.

PhosphaBase is an ontology-driven database resource containing information on the protein phosphatase family. It is the first public resource dedicated to protein phosphatases, which are enzymes that perform dephosphorylation reactions. In conjunction with the phosphorylation action of protein kinases, phosphatases are involved in important control and communication mechanisms in the cell. They have also been implicated in many human diseases, including diabetes and obesity, cancers, and neurodegenerative conditions. PhosphaBase aims to centralize the growing base of knowledge in the phosphatase research domain. The resource is built around a formal, domain-specific DAML+OIL ontology, and the data are collected from heterogeneous biological sources using Gene Ontology terms as a means of data extraction. The overall ontology-driven architecture provides a robust structure with distinct advantages for sustainability and provides the potential for the development of diagnostic tools, as well as a data repository.

Animals↗

PubMed1996

The Blocks database--a system for protein classification.

The Blocks Database contains multiple alignments of conserved regions in protein families. The database can be searched by e-mail and World Wide Web(WWW) servers (http://blocks.fhcrc.org/help) to classify protein and nucleotide sequences.

Amino Acid Sequence↗

PubMed2004

UniProt archive.

UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant, publicly accessible resources. All new and updated protein sequences are collected and loaded daily into UniParc for full coverage. To avoid redundancy, each unique sequence is stored only once with a stable protein identifier, which can be used later in UniParc to identify the same protein in all source databases. When proteins are loaded into the database, database cross-references are created to link them to the origins of the sequences. As a result, performing a sequence search against UniParc is equivalent to performing the same search against all databases cross-referenced by UniParc. UniParc contains only protein sequences and database cross-references; all other information must be retrieved from the source databases.

Amino Acid Sequence↗

PubMed2003

Gene discovery in Eimeria tenella by immunoscreening cDNA expression libraries of sporozoites and schizonts with chicken intestinal antibodies.

Specific antibodies were produced ex vivo from intestinal culture of Eimeria tenella infected chickens. The specificity of these intestinal antibodies was tested against different parasite stages. These antibodies were used to immunoscreen first generation schizont and sporozoite cDNA libraries permitting the identification of new E. tenella antigens. We obtained a total of 119 cDNA clones which were subjected to sequence analysis. The sequences coding for the proteins inducing local immune responses were compared with nucleotide or protein databases and with expressed sequence tags (ESTs) databases. We identified new Eimeria genes coding for heat shock proteins, a ribosomal protein, a pyruvate kinase and a pyridoxine kinase. Specific features of other sequences are discussed.

Animals↗