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PubMed2004

Molecular cloning and characterization of a glutathione S-transferase from largemouth bass (Micropterus salmoides) liver that is involved in the detoxification of 4-hydroxynonenal.

We are currently investigating the role of detoxification pathways in protecting against the sublethal effects of chemicals in largemouth bass (Micropterus salmoides). To this end, previous work in our laboratory indicated a remarkable ability of bass liver glutathione S-transferases (GSTs) to detoxify 4-hydroxynonenal (4HNE), a common mutagenic and cytotoxic alpha,beta-unsaturated aldehyde produced during the peroxidation of lipids. In the current study, we observed that GST-mediated 4HNE conjugation in bass liver follows high efficiency single-enzyme Michaelis-Menten kinetics, suggesting that an individual GST isoform is involved in 4HNE detoxification. Using 5' and 3' rapid amplification of cDNA ends (RACE), a full-length GST cDNA of 957 base pairs (bp) in length, containing an open reading frame of 678 bp and encoding a polypeptide of 225 amino acids, has been cloned. Interestingly, a search of the BLAST protein database revealed the presence of homologous GST proteins in the plaice (Pleuronectes platessa), European flounder (Platichthys flesus) and fathead minnow (Pimephales promelas), but not in other fish species. Furthermore, the bass GST protein exhibited little homology with the mammalian GSTA4 subclass of proteins which rapidly metabolize 4HNE. The recombinant 6 x His-tagged expressed GST protein showed high catalytic activity towards 4HNE, while showing moderate or low activity toward other class specific GST substrates. HPLC-GST subunit analysis, followed by sequencing, demonstrated that the isolated bass liver GST subunit constitutes the major GST protein in bass liver, with a molecular mass of 26.4 kDa. In summary, the presence of a highly expressed GST isozyme in bass and several evolutionarily divergent fish species indicates the conservation of an important and distinct detoxification protein that protects against oxidative damage in certain aquatic organisms.

Amino Acid Sequence↗

PubMed2005

Functional proteome of bones in rats with osteoporosis following ovariectomy.

Osteoporosis is a chronic condition chiefly affecting postmenopausal women, in whom the skeleton loses a significant percentage of its mineralized mass and mechanical resiliency, thereby becoming prone to fracture. Although the effect of the loss of estrogen on bone metabolism has been documented, its mechanism is still poorly understood. In the present proteomic study, we characterized the effect of estrogen deficiency on protein expression in rat bones. Using two-dimensional gel electrophoresis, mass spectrometry and rat protein database, we successfully identified three distinctly changed proteins named thioredoxin peroxidase 1, myosin light polypeptide 2 and ubiquitin-conjugating enzyme E2-17 kD, among which ubiquitin-conjugating enzyme E2-17 kD has been documented to be an estrogen-related protein, but the other two are first reported to be osteoporosis-related proteins in the current study. These results provide valuable experimental evidences for the elucidation of the molecular mechanism of osteoporosis related to the loss of estrogen.

Animals↗

PubMed2006

Piecing together a ciliome.

Cilia are slender microtubule-based appendages that emanate from the surfaces of a large proportion of eukaryotic cells. The motile and non-motile forms of cilia represent bona fide organelles comprising distinct repertoires of proteins that serve specific roles in locomotion or fluid movement, and sense chemical or physical extracellular cues. Owing in part to the growing number of genes associated with ciliary disorders, such as polycystic kidney disease and Bardet-Biedl syndrome, there has been a recent profusion of studies aimed at unveiling the protein makeup of cilia. The approaches used are complementary, involving several different organisms and spanning the fields of bioinformatics, genomics and proteomics. Here we review these studies and assess the various data sets to help define a comprehensive ciliary proteome, or 'ciliome'. We have compiled a cilia protein database that includes known cilia-associated proteins and numerous putative ciliary proteins including RAB-like small GTPases, which might be implicated in vesicular trafficking, and the microtubule-binding protein MIP-T3, some of which might be associated with ciliopathies.

Animals↗

PubMed2006

Using capillary electrophoresis-selective tandem mass spectrometry to identify pathogens in clinical samples.

Analysis of microbial mixtures in complex systems, such as clinical samples, using mass spectrometry can be challenging because the specimens may contain mixtures of several pathogens or both pathogens and nonpathogens. We have successfully applied capillary electrophoresis-selective MS/MS of unique peptide marker ions to the identification of common pathogens in clinical diagnosis. We searched the CE-MS/MS spectra acquired from the proteolytic digests of pure bacterial cell extracts against protein databases. The identified peptides that matched a protein associated with a particular pathogen were selected as marker ions to identify that bacterium in clinical specimens. Thirty-four clinical specimens, obtained from pus, wound, sputum, and urine samples, were analyzed using both biochemical and selective MS/MS methods. The bacteria in these clinical samples were cultivated directly, without prior isolation of a pure colony, before performing the selective MS/MS analyses. The bacteria analyzed included both Gram-positive and -negative strains. The match with respect to the pathogens identified was good between the biochemical and the selective MS/MS methods; the matching rate was 91%. The rate was as high as 97% when not considering two specimens for which the bacteria were not grown successfully. Two of the specimens that we identified using the biochemical method as containing two bacterial species were confirmed also through selective tandem MS analysis.

Electrophoresis, Capillary↗

PubMed2002

Antiviral and antitumor peptides from insects.

Insects can rapidly clear microbial infections by producing a variety of immune-induced molecules including antibacterial and/or antifungal peptides/polypeptides. In this report, we present the isolation, structural characterization, and biological properties of two variants of a group of bioactive, slightly cationic peptides, referred to as alloferons. Two peptides were isolated from the blood of an experimentally infected insect, the blow fly Calliphora vicina (Diptera), with the following amino acid sequences: HGVSGHGQHGVHG (alloferon 1) and GVSGHGQHGVHG (alloferon 2). Although these peptides have no clear homologies with known immune response modifiers, protein database searches established some structural similarities with proteins containing amino acid stretches similar to alloferon. In vitro experiments reveal that the synthetic version of alloferon has stimulatory activities on natural killer lymphocytes, whereas in vivo trials indicate induction of IFN production in mice after treatments with synthetic alloferon. Additional in vivo experiments in mice indicate that alloferon has antiviral and antitumoral capabilities. Taken together, these results suggest that this peptide, which has immunomodulatory properties, may have therapeutic capacities. The fact that insects may produce cytokine-like materials modulating basic mechanisms for human immunity suggests a source of anti-infection and antitumoral biopharmaceuticals.

Amino Acid Sequence↗

PubMed1999

Tyrosine phosphorylation of alpha-actinin in activated platelets.

The integrin alpha(IIb)beta(3) mediates tyrosine phosphorylation of a 105-kDa protein (pp105) in activated platelets. We have partially purified a 105-kDa tyrosine-phosphorylated protein from platelets stimulated with phorbol 12-myristate 13-acetate and obtained the sequence of an internal 12-mer peptide derived from this protein. The sequence was identical to human alpha-actinin sequences deposited in the Swiss Protein Database. alpha-Actinin, a 105-kDa protein in platelets, was subsequently purified from activated platelets by four sequential chromatographic steps. Fractions were analyzed by Western blotting and probed with alpha-actinin and anti-phosphotyrosine antibodies. The distribution of alpha-actinin and pp105 overlapped throughout the purification. Furthermore, in the course of this purification, a 105-kDa tyrosine-phosphorylated protein was only detected in fractions that contained alpha-actinin. The purified alpha-actinin protein was immunoprecipitated with antibodies to phosphotyrosine in the absence but not in the presence of phenyl phosphate. alpha-Actinin resolved by two-dimensional gel electrophoresis of activated platelet lysates was recognized by the antibodies to phosphotyrosine, whereas pretreatment of the platelets with bisindolylmaleimide, a protein kinase C inhibitor that prevents tyrosine phosphorylation of pp105, inhibited the reactivity of the antibodies to phosphotyrosine with alpha-actinin. Taken together, these data demonstrate that a fraction of alpha-actinin is tyrosine-phosphorylated in activated platelets.

Actinin↗

PubMed1995

Mastering the LORE of protein structure.

A detailed description of the design, operation and capabilities of LORE, a protein-database management tool to supplement more traditional protein map-fitting and model-building programs, is presented. The program includes elements for searching the library of known crystal structures for substructures of similar geometry. Substructures may be as simple as a single hairpin turn, or as complicated as an assembly of different elements of secondary structure. The programs also include elements for manipulating structural segments in complex ways to enable a sophisticated molecular editing capability of enormous utility in modeling and structure-refinement applications.

Journal Article↗

PubMed2005

Prediction of functional class of novel plant proteins by a statistical learning method.

In plant genomes, the function of a substantial percentage of the putative protein-coding open reading frames (ORFs) is unknown. These ORFs have no significant sequence similarity to known proteins, which complicates the task of functional study of these proteins. Efforts are being made to explore methods that are complementary to, or may be used in combination with, sequence alignment and clustering methods. A web-based protein functional class prediction software, SVMProt, has shown some capability for predicting functional class of distantly related proteins. Here the usefulness of SVMProt for functional study of novel plant proteins is evaluated. To test SVMProt, 49 plant proteins (without a sequence homolog in the Swiss-Prot protein database, not in the SVMProt training set, and with functional indications provided in the literature) were selected from a comprehensive search of MEDLINE abstracts and Swiss-Prot databases in 1999-2004. These represent unique proteins the function of which, at present, cannot be confidently predicted by sequence alignment and clustering methods. The predicted functional class of 31 proteins was consistent, and that of four other proteins was weakly consistent, with published functions. Overall, the functional class of 71.4% of these proteins was consistent, or weakly consistent, with functional indications described in the literature. SVMProt shows a certain level of ability to provide useful hints about the functions of novel plant proteins with no similarity to known proteins.

Artificial Intelligence↗

PubMed2003

Characterization of proteins responsive to gibberellin in the leaf-sheath of rice (Oryza sativa L.) seedling using proteome analysis.

In plants gibberellins (GAs) are responsible for triggering stem or internodal elongation. To comprehend the molecular basis of internodal elongation in rice, a proteomics approach using differentially displayed proteins on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was carried out to identify the proteins expressed during the GA controlled leaf-sheath elongation response. Out of 352 protein spots detected on 2-D PAGE, 32 proteins showed modulation in the expression levels in GA3-treated leaf-sheath for 48 h as compared to control. These proteins were analyzed using protein sequencer and/or mass spectrometry in conjunction with the protein database to assign putative identities. The twin protein spots (LS079 and LS083), identified as calreticulin, showed different isoelectric points and expression level in GA3-treated leaf-sheath. The expression level of LS083 (pI 4.0) was down-regulated as compared to the up-regulation of LS079 (pI 4.3). In the presence of GA3 and growth inhibitor, uniconazole and abscisic acid, respectively, no elongation in leaf-sheath occurred and calreticulin did not shift from LS083 to LS079. Over-expression of calreticulin in rice inhibited the callus regeneration and seedling growth. These results suggest that calreticulin is an important component in the GA signaling pathway that regulates rice seedling leaf-sheath elongation.

Amino Acid Sequence↗

PubMed1992

A homologue of the Drosophila female sterile homeotic (fsh) gene in the class II region of the human MHC.

The RING3 gene maps in the class II region of the human major histocompatibility complex, at a CpG island distal of the HLA-DNA gene. RING3 cDNAs were obtained from a T cell cDNA library and the longest (4 kb) was sequenced. The sequence contained an open reading frame encoding a protein of 754 amino acids. A screen of protein databases revealed striking homology between the RING3 protein and the Drosophila female sterile homeotic gene (fsh) which is implicated in the establishment of segments in the early embryo. Partial sequence homology was also observed with some other proteins involved in cell cycle control (CCG1), cell division (ftsA) and regulation of cell growth (gamma interferons). This highly conserved gene may play an important role in human development. In addition, its location in the MHC class II region may be related to some HLA-associated diseases.

Amino Acid Sequence↗

PubMed1992

Secondary structure analysis identifies a putative mouse protein demonstrating similarity to the repeat units found in CDC4, the G protein beta subunits and related proteins.

The predicted protein product of an anonymous clone isolated from a cDNA library prepared from 12 day post coitum (p.c) embryonic mouse heart tissue demonstrated the same segmental repeats previously identified in the cell division control protein, CDC4 and the G protein beta 1 subunit. A search of the protein database subsequently identified three other classes of protein containing the repeat. Secondary structure analyses performed on the repeat sequences revealed a high degree of conservation suggesting that the repeat motif performs a specific function in a diverse range of proteins.

Amino Acid Sequence↗

PubMed1991

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

The problem of constructing all-atom model co-ordinates of a protein from an outline of the polypeptide chain is encountered in protein structure determination by crystallography or nuclear magnetic resonance spectroscopy, in model building by homology and in protein design. Here, we present an automatic procedure for generating full protein co-ordinates (backbone and, optionally, side-chains) given the C alpha trace and amino acid sequence. To construct backbones, a protein structure database is first scanned for fragments that locally fit the chain trace according to distance criteria. A best path algorithm then sifts through these segments and selects an optimal path with minimal mismatch at fragment joints. In blind tests, using fully known protein structures, backbones (C alpha, C, N, O) can be reconstructed with a reliability of 0.4 to 0.6 A root-mean-square position deviation and not more than 0 to 5% peptide flips. This accuracy is sufficient to identify possible errors in protein co-ordinate sets. To construct full co-ordinates, side-chains are added from a library of frequently occurring rotamers using a simple and fast Monte Carlo procedure with simulated annealing. In tests on X-ray structures determined at better than 2.5 A resolution, the positions of side-chain atoms in the protein core (less than 20% relative accessibility) have an accuracy of 1.6 A (r.m.s. deviation) and 70% of chi 1 angles are within 30 degrees of the X-ray structure. The computer program MaxSprout is available on request.

Algorithms↗

PubMedDate not supplied

Development of two novel CYP-antibodies and their use in a PCB exposure experiment with Mytilus edulis.

In an attempt to learn more about the cytochrome P450 (CYP) system of mussels, we used protein databases and alignment software to extract highly conserved CYP sequences. From these alignments synthetic peptides were produced and used for rabbit immunisation, which yielded polyclonal antibodies against the CYP families 2 and 4. The antibodies were evaluated with Western Blot and ELISA assays, using digestive gland microsomal samples from the mussel Mytilus edulis. Western Blots revealed immunoreactions for both antibodies. The anti-CYP2 sequence rendered one major immunopositive protein of approximately 49 kDa size, and weak signals for proteins of approximately 41 and 56 kDa size. The anti-CYP4 sequence rendered two major bands of approximately 56 and 59 kDa size, and also a weak immunoreaction with a protein of approximately 43 kDa size. ELISA rendered only weak signals even with a 1:50 dilution of IgG-purified serum. A 10-day exposure to Aroclor 1254 did not appear to affect any of the immunopositive proteins, while total PCBs in soft bodies increased from 14-40 ng/g DW in controls to 373-638 ng/g DW in exposed mussels.

Amino Acid Sequence↗

PubMed1996

YPD-A database for the proteins of Saccharomyces cerevisiae.

YPD is a database for the proteins of the budding yeast, Saccharomyces cerevisiae. YPD has two formats: (i) a spreadsheet which tabulates many of the physical and functional properties of yeast proteins, and (ii) the YPD Protein Reports which are formatted pages containing the protein properties, annotations gathered from the literature, and references with titles. YPD is available through the World-Wide Web, through an Email server, and by anonymous FTP. New releases of the YPD spreadsheet are produced every two to four months, and the on-line information is updated daily.

Computer Communication Networks↗

PubMed2005

Building a protein name dictionary from full text: a machine learning term extraction approach.

BACKGROUND: The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. RESULTS: We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. CONCLUSION: This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt.

Abstracting and Indexing↗

PubMed1998

Two-dimensional gel analysis of proteins in the Drosophila wing imaginal disc mutants fat and lethal (2) giant discs.

High-resolution two-dimensional (2D) gel electrophoresis coupled with computer analysis has been used to construct a quantitative protein database of Drosophila mature wing imaginal discs. The level of expression for all of the detected proteins has been quantitatively determined. This database has been used to evaluate changes in the patterns of protein synthesis in wing imaginal discs from two Drosophila melanogaster mutants with abnormal wing disc development: fat (ft) and two different alleles of lethal (2) giant disc (l(2)gd). Patterns of pulse-labeled proteins of the different mutants show variations in both qualitative and quantitative parameters of synthesis. In this comparison we have detected specific sets of protein changes characteristic of both alleles of the same locus and a set of protein changes common to both loci. How the abnormal expression of these proteins relates to the abnormal process of mutant hyperplasia is discussed.

Animals↗

PubMed2004

Accurate classification of protein structural families using coherent subgraph analysis.

Protein structural annotation and classification is an important problem in bioinformatics. We report on the development of an efficient subgraph mining technique and its application to finding characteristic substructural patterns within protein structural families. In our method, protein structures are represented by graphs where the nodes are residues and the edges connect residues found within certain distance from each other. Application of subgraph mining to proteins is challenging for a number reasons: (1) protein graphs are large and complex, (2) current protein databases are large and continue to grow rapidly, and (3) only a small fraction of the frequent subgraphs among the huge pool of all possible subgraphs could be significant in the context of protein classification. To address these challenges, we have developed an information theoretic model called coherent subgraph mining. From information theory, the entropy of a random variable X measures the information content carried by X and the Mutual Information (MI) between two random variables X and Y measures the correlation between X and Y. We define a subgraph X as coherent if it is strongly correlated with every sufficiently large sub-subgraph Y embedded in it. Based on the MI metric, we have designed a search scheme that only reports coherent subgraphs. To determine the significance of coherent protein subgraphs, we have conducted an experimental study in which all coherent subgraphs were identified in several protein structural families annotated in the SCOP database (Murzin et al, 1995). The Support Vector Machine algorithm was used to classify proteins from different families under the binary classification scheme. We find that this approach identifies spatial motifs unique to individual SCOP families and affords excellent discrimination between families.

Algorithms↗

PubMed2002

Glycosylation of proteins: a computer based method for the rapid exploration of conformational space of N-glycans.

Inspection of protein databases suggests that as many as 70% of proteins have potential N-glycosylation sites. Unfortunately glycoproteins often refuse to crystallize and NMR techniques do not allow an unambiguous determination of the complete conformation of the sugar part. Therefore, time-consuming complex simulation methods are often used to explore the conformational space of N-glycans. The generation of a comprehensive data base describing the conformational space of larger fragments of N-glycans taking into account the effects of branching is presented. High-temperature molecular dynamics simulations of essential N-glycan fragments are performed until conformational equilibrium has been reached. Free energy landscapes are calculated for each glycosidic linkage. All possible conformations for each N-glycan fragment are automatically assigned, ranked according to their relative population and stored in a database. These values are recalled for the generation of a complete set of all possible conformations for a given N-glycan topology. The constructed conformations are ranked according to their energy content. Since this approach allows to explore the complete conformational space of a given N-glycan within a few minutes of CPU-time on a standard PC, it is well suited to be used as a Web-Based application.

Carbohydrate Conformation↗