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PubMed2001

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

Databases, Factual↗
PubMed1982

Design and implementation of a prototype Human Protein Index.

This paper describes information-handling aspects of the TYCHO I analysis system (Clin, Chem. 27: 1807--1820, 1981), which analyzes two-dimensional electrophoresis gels, matches the individual protein spots with those in a reference pattern, and stores various information--including spot measurements, identifications, treatment profiles, set memberships, and comments--in a computerized database. This and additional information such as amino acid composition and cellular localization is then accessible from an interactive program that includes a pictorial user interface and presents much of the data in graphical form. Use of the TYCHO I system is illustrated by examples drawn from analyses of gel patterns from human leukocytes.

Blood Proteins↗
PubMed2000

Identification of proteassemblin, a mammalian homologue of the yeast protein, Ump1p, that is required for normal proteasome assembly.

We have identified a mammalian homologue of yeast Ump1p by searching for similar proteins in human and mouse expressed sequence tag (EST) databases. Ump1p is an accessory protein that is required for normal proteasome assembly in yeast (1). A mammalian homologue, which we refer to as "proteassemblin," is a constituent of proteasome assembly intermediates (preproteasomes), but not fully assembled 20S proteasomes, as is Ump1p in yeast. We also provide evidence that proteassemblin is a constituent of pre-immunoproteasomes that contain the precursor of the interferon-gamma-inducible subunit LMP2. By analogy with Ump1p, we hypothesize that proteassemblin is required for normal mammalian proteasome assembly.

Amino Acid Sequence↗
PubMed2002

Novel odorant-binding proteins expressed in the taste tissue of the fly.

A taste tissue cDNA library of the fleshfly Boettcherisca peregrina was screened with a subtracted cDNA probe enriched with taste-receptor-tissue-specific cDNA. Seven genes were identified with sequence similarity to insect odorant-binding protein (OBP) genes. The predicted amino acid sequences of the genes contain the putative signal peptide sequence at the N-terminal and most of them conserve the six cysteines common to known insect OBPs. These genes show a high degree of sequence divergence with approximately 20% amino acid identity. The most striking feature was that all seven of these genes are expressed mainly in the taste tissues, such as the labellum and tarsus, unlike the known insect OBP genes expressed in olfactory tissue. The predicted amino acid sequences had the highest degree of sequence similarity to the Drosophila melanogaster OBPs named pheromone binding protein-related proteins (PBPRPs). These gene products are here referred to as gustatory PBP-related proteins (GPBPRPs) 1-7. Homologous GPBPRP genes were found also in D. melanogaster by database search and are shown to be expressed in Drosophila taste tissues.

Amino Acid Sequence↗
PubMed2000

Cloning and expression of CIS6, chromosome assignment to 3p22 and 2p21 by in situ hybridization.

A family of negative regulators of JAK signaling pathway referred to as suppressor of cytokines signaling (SOCS) or cytokine-inducible SH2 protein (CIS) has been recently identified. In order to find additional members of this family, we have used a consensus amino acid sequence contained in the well-conserved central SH2 domain to search DNA databases. We isolated cDNA coding for the human homologue of SOCS-5, referred to as CIS6. Northern blot analysis revealed CIS6 mRNA expression in various tissues such as heart, muscle, spleen, and thymus and in all myeloma cell lines examined. The gene was assigned to human chromosome bands 2p21 and 3p22 by in situ hybridization. CIS6 is structurally related to other members of the CIS family and therefore could act as a negative regulator of signal transduction.

Amino Acid Sequence↗
PubMed1997

Does conformational free energy distinguish loop conformations in proteins?

Limitations in protein homology modeling often arise from the inability to adequately model loops. In this paper we focus on the selection of loop conformations. We present a complete computational treatment that allows the screening of loop conformations to identify those that best fit a molecular model. The stability of a loop in a protein is evaluated via computations of conformational free energies in solution, i.e., the free energy difference between the reference structure and the modeled one. A thermodynamic cycle is used for calculation of the conformational free energy, in which the total free energy of the reference state (i.e., gas phase) is the CHARMm potential energy. The electrostatic contribution of the solvation free energy is obtained from solving the finite-difference Poisson-Boltzmann equation. The nonpolar contribution is based on a surface area-based expression. We applied this computational scheme to a simple but well-characterized system, the antibody hypervariable loop (complementarity-determining region, CDR). Instead of creating loop conformations, we generated a database of loops extracted from high-resolution crystal structures of proteins, which display geometrical similarities with antibody CDRs. We inserted loops from our database into a framework of an antibody; then we calculated the conformational free energies of each loop. Results show that we successfully identified loops with a "reference-like" CDR geometry, with the lowest conformational free energy in gas phase only. Surprisingly, the solvation energy term plays a confusing role, sometimes discriminating "reference-like" CDR geometry and many times allowing "non-reference-like" conformations to have the lowest conformational free energies (for short loops). Most "reference-like" loop conformations are separated from others by a gap in the gas phase conformational free energy scale. Naturally, loops from antibody molecules are found to be the best models for long CDRs (> or = 6 residues), mainly because of a better packing of backbone atoms into the framework of the antibody model.

Antibodies↗
PubMed2000

Protein supplementation of human milk for promoting growth in preterm infants.

BACKGROUND: For term infants, human milk provides adequate nutrition to facilitate growth, as well as potential beneficial effects on immunity and the maternal-infant emotional state. However, the role of human milk in preterm infants is less well defined as it contains insufficient quantities of some nutrients to meet the estimated needs of the infant. Preterm infants require higher protein intakes than term infants to attain adequate growth rates, and have relatively higher protein turnover rates. Inadequate protein intakes may be partly responsible for low serum albumin and blood urea concentrations in preterm infants. OBJECTIVES: The main objective was to determine if addition of protein to human milk leads to improved growth and neurodevelopmental outcomes without significant adverse effects in preterm infants. SEARCH STRATEGY: The standard search strategy of the Cochrane Neonatal Review Group was used. This includes searches of the Oxford Database of Perinatal Trials, MEDLINE, previous reviews including cross references, abstracts, conferences and symposia proceedings, expert informants, and journal handsearching mainly in the English language. SELECTION CRITERIA: All trials utilizing random or quasi-random allocation to supplementation of human milk with protein or no supplementation in preterm infants who remained in hospital were eligible. DATA COLLECTION AND ANALYSIS: Data were extracting using the standard methods of the Cochrane Neonatal Review Group, with separate evaluation of trial quality and data extraction by each author and synthesis of data using relative risk and weighted mean difference. MAIN RESULTS: Protein supplementation of human milk results in increases in short term weight gain (WMD 3.6 g/kg/day, 95% CI 2.4 to 4.8 g/kg/day), linear growth (WMD 0.28 cm/week, 95% CI 0.18 to 0.38 cm/week) and head growth (WMD 0.15 cm/week, 95% CI 0.06 to 0.23 cm/week). There are insufficient data to evaluate long term neurodevelopmental and growth outcomes. There are too few infants studied to be certain that adverse effects of protein supplementation are not increased. Blood urea levels are increased (WMD 1.0 mmol/l, 95% CI 0.8 to 1.2 mmol/l). REVIEWER'S CONCLUSIONS: Protein supplementation of human milk in relatively well preterm infants results in increases in short term weight gain, linear and head growth. Urea levels are increased, which may reflect adequate rather than excessive dietary protein intake. Further research should be directed towards the evaluation of specific levels of protein intake in preterm infants and the clinical effects of supplementation with protein, including long term growth and neurodevelopmental outcomes. This may best be done in the context of refinement of available multicomponent fortifier preparations.

Dietary Proteins↗
PubMed1985

ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage.

ACNUC is a database structure and retrieval software for use with either the GenBank or EMBL nucleic acid sequence data collections. The nucleotide and textual data furnished by both collections are each restructured into a database that allows sequence retrieval on a multi-criterion basis. The main selection criteria are: species (or higher order taxon), keyword, reference, journal, author, and organelle; all logical combinations of these criteria can be used. Direct access to sequence regions that code for a specific product (protein, tRNA or rRNA) is provided. A versatile extraction procedure copies selected sequences, or fragments of them, from the database to user files suitable to be analysed by user-supplied application programs. A detailed help mechanism is provided to aid the user at any time during the retrieval session. All software has been written in FORTRAN 77 which guarantees a high degree of transportability to minicomputers or mainframes.

Base Sequence↗
PubMed2002

YPL.db: the Yeast Protein Localization database.

The Yeast Protein Localization database (YPL.db) contains information about the localization patterns of yeast proteins resulting from microscopic analyses. The data and parameters of the experiments to obtain the localization information, together with images from confocal or video microscopy, are stored in a relational database, building an archive of, and the documentation for, all experiments. The database can be queried based on gene name, protein localization, growth conditions and a number of additional parameters. All experiment parameters are selectable from predefined lists to ensure database integrity and conformity across different investigators. The database provides a structure reference resource to allow for better characterization of unknown or ambiguous localization patterns. Links to MIPS, YPD and SGD databases are provided to allow fast access to further information not contained in the localization database itself. YPL.db is available at http://ypl.tugraz.at.

Computer Graphics↗
PubMed1995

Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions.

An algorithm is presented for the fast and accurate definition of protein structural domains from coordinate data without prior knowledge of the number or type of domains. The algorithm explicitly locates domains that comprise one or two continuous segments of protein chain. Domains that include more than two segments are also located. The algorithm was applied to a nonredundant database of 230 protein structures and the results compared to domain definitions obtained from the literature, or by inspection of the coordinates on molecular graphics. For 70% of the proteins, the derived domains agree with the reference definitions, 18% show minor differences and only 12% (28 proteins) show very different definitions. Three screens were applied to identify the derived domains least likely to agree with the subjective definition set. These screens revealed a set of 173 proteins, 97% of which agree well with the subjective definitions. The algorithm represents a practical domain identification tool that can be run routinely on the entire structural database. Adjustment of parameters also allows smaller compact units to be identified in proteins.

Actins↗
PubMed2000

Protein analysis by mass spectrometry and sequence database searching: a proteomic approach to identify human lymphoblastoid cell line proteins.

Lymphoblastoid cell lines correspond to in vitro EBV-immortalized lymphocyte B-cells. These cells display a suitable model for experiments dealing with changes in protein expression occurring upon B-cell differentiation, after drug treatment, or after inhibition of some transcription factors. For all these reasons we have undertaken an effort aimed at developing a hematopoietic cell line protein two-dimensional electrophoresis (2-DE) database, containing B-lymphoblastoid 2-DE maps. In this work, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) peptide mass fingerprinting analysis was adopted for protein identification. The peptide mass fingerprinting identification and the sequence coverage obtained on colloidal Coomassie blue (CBB) stained gel was close to that obtained using zinc-imidazole staining. Everything considered, CBB being more comfortable for subsequent spot manipulations, CBB staining was chosen for identification of a larger number of polypeptides. The results suggest that reticulation of the gel can interfere preventing the uptake of the enzyme during the in-gel digestion step. Consequently, low molecular mass proteins appear more difficult to identify by mass fingerprinting. Finally, the information provided in this study allows the construction of a new annoted reference map of human lymphoblastoid cell proteins. Among the identified proteins 60% were not yet positioned on 2-DE maps in three of the most important well-documented databases. The annoted map will be accessible via Internet on the LBPP server at URL:http:// www-smbh.univ-paris13.fr/lbtp/index.htm.

Acrylic Resins↗
PubMed2000

CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000.

CyanoBase provides an online resource for access to data on genomic information about the cyanobacterium Synechocystis sp. strain PCC6803. The database contains annotations for each protein-coding gene deduced from the entire nucleotide sequence of the genome, gene classification lists, and keyword and similarity search engines. Core portions of CyanoBase consist of annotations for each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. The contents of each gene were improved by updating with the results of similarity searches and by introducing references for analysis in bioinformatics. The database now contains repository facilities that store and provide experimental information, in addition to providing proposals for the function of each gene. This information should help to avoid unnecessary, overlapping experiments and should assist communication between scientists who wish to elucidate the function of putative genes on the cyanobacteria genome. The current URL of CyanoBase is http://www.kazusa.or.jp:8080/cyano/

Cyanobacteria↗
PubMed1992

The ICOH and IUPAC international programme for establishing reference values of metals.

In cooperation with the ICOH Scientific Committee on the Toxicology of metals and IUPAC Commission on Toxicology, we have developed evaluation criteria for derivation of reference values for metal concentrations in human tissues and fluids. In a first attempt to illustrate how these criteria may be used, tentative reference values for mercury in human blood were derived. For persons who do not eat fish, a mean value of 10 mumol/1 (2 micrograms/1) was suggested. It was pointed out, however, that this value was based on information that did not meet the desired quality requirements, which, unfortunately were not met by any of the published reports.

Animals↗
PubMed2000

Sequence database search using jumping alignments.

We describe a new algorithm for amino acid sequence classification and the detection of remote homologues. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a well balanced manner. This is in contrast to established methods like profiles and hidden Markov models which focus on vertical information as they model the columns of the alignment independently. In our setting, we want to select from a given database of "candidate sequences" those proteins that belong to a given superfamily. In order to do so, each candidate sequence is separately tested against a multiple alignment of the known members of the superfamily by means of a new jumping alignment algorithm. This algorithm is an extension of the Smith-Waterman algorithm and computes a local alignment of a single sequence and a multiple alignment. In contrast to traditional methods, however, this alignment is not based on a summary of the individual columns of the multiple alignment. Rather, the candidate sequence at each position is aligned to one sequence of the multiple alignment, called the "reference sequence". In addition, the reference sequence may change within the alignment, while each such jump is penalized. To evaluate the discriminative quality of the jumping alignment algorithm, we compared it to hidden Markov models on a subset of the SCOP database of protein domains. The discriminative quality was assessed by counting the number of false positives that ranked higher than the first true positive (FP-count). For moderate FP-counts above five, the number of successful searches with our method was considerably higher than with hidden Markov models.

Animals↗
PubMed2000

CCR9A and CCR9B: two receptors for the chemokine CCL25/TECK/Ck beta-15 that differ in their sensitivities to ligand.

We isolated cDNAs for a chemokine receptor-related protein having the database designation GPR-9-6. Two classes of cDNAs were identified from mRNAs that arose by alternative splicing and that encode receptors that we refer to as CCR9A and CCR9B. CCR9A is predicted to contain 12 additional amino acids at its N terminus as compared with CCR9B. Cells transfected with cDNAs for CCR9A and CCR9B responded to the chemokine CC chemokine ligand 25 (CCL25)/thymus-expressed chemokine (TECK)/chemokine beta-15 (CK beta-15) in assays for both calcium flux and chemotaxis. No other chemokines tested produced responses specific for the cDNA-transfected cells. mRNA for CCR9A/B is expressed predominantly in the thymus, coincident with the expression of CCL25, and highest expression for CCR9A/B among thymocyte subsets was found in CD4+CD8+ cells. mRNAs encoding the A and B forms of the receptor were expressed at a ratio of approximately 10:1 in immortalized T cell lines, in PBMC, and in diverse populations of thymocytes. The EC50 of CCL25 for CCR9A was lower than that for CCR9B, and CCR9A was desensitized by doses of CCL25 that failed to silence CCR9B. CCR9 is the first example of a chemokine receptor in which alternative mRNA splicing leads to proteins of differing activities, providing a mechanism for extending the range of concentrations over which a cell can respond to increments in the concentration of ligand. The study of CCR9A and CCR9B should enhance our understanding of the role of the chemokine system in T cell biology, particularly during the stages of thymocyte development.

Alternative Splicing↗
PubMed2001

African swine fever virus-induced polypeptides in porcine alveolar macrophages and in Vero cells: two-dimensional gel analysis.

High-resolution two-dimensional electrophoresis followed by computer analysis has been used to study quantitatively the patterns of protein synthesis produced in porcine alveolar macrophages and in Vero cells infected with African swine fever virus (ASFV). Initially, a protein database for each cell type was constructed. The porcine alveolar macrophage database includes 995 polypeptides (818 acidic, isoelectric focusing (IEF) and 177 basic, nonequilibrium pH gradient electrophoresis (NEPHGE)) whereas the Vero database contains 1,398 polypeptides (1,127 acidic, IEF and 271 basic, NEPHGE). Taking these databases as reference, ASFV highly virulent strain E70 induces 57 acid and 43 basic polypeptides in porcine alveolar macrophages, which account for most of the information content of the virus DNA. The kinetics of synthesis of the virus-induced polypeptides showed the existence of three classes of proteins: one whose synthesis starts early after infection, continues for a period and then switches off; another whose synthesis also starts early but continues for prolonged periods; and a third which requires DNA replication. The attenuated, cell adapted, strain BA71V induces 92 acidic and 37 basic proteins in Vero cells. Significant differences were observed when comparing the patterns of polypeptides induced by the two viral strains. In both cell systems studied, ASFV infection produces a general shutoff of protein synthesis that affects up to 65% of the cellular proteins. Interestingly, 28 proteins of porcine alveolar macrophages and 48 proteins of Vero cells are stimulated at least two times by ASFV infection.

African Swine Fever Virus↗
PubMed1997

SCOP: a structural classification of proteins database.

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. SCOP also provides for each structure links to atomic co-ordinates, images of the structures, interactive viewers, sequence data, data on any conformational changes related to function and literature references. The database is freely accessible on the World Wide Web (WWW) with an entry point at URL http://scop.mrc-lmb.cam.ac.uk/scop/

Amino Acid Sequence↗