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PubMed2005

SPD--a web-based secreted protein database.

With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They were further annotated via a proteome annotation pipeline that we developed. We also set up a secreted protein classification pipeline and classified our predicted secreted proteins into different functional categories. To make the dataset more convincing and comprehensive, nine reference datasets are also integrated, such as the secreted proteins from the Gene Ontology Annotation (GOA) system at the European Bioinformatics Institute, and the vertebrate secreted proteins from Swiss-Prot. All these entries were grouped via a TribeMCL based clustering pipeline. We have constructed a web-based secreted protein database, which has been publicly available at http://spd.cbi.pku.edu.cn. Users can browse the database via a GO assignment or chromosomal-location-based interface. Moreover, text query and sequence similarity search are also provided, and the sequence and annotation data can be downloaded freely from the SPD website.

Animals↗
PubMed2000

Proteome analysis of mouse brain: two-dimensional electrophoresis profiles of tissue proteins during the course of aging.

Mouse brain proteins were isolated from five regions (cerebellum, cerebral cortex, hippocampus, striatum, and cervical spinal cord) at five ages from the 10th week to the 24th month, and separated by two-dimensional gel electrophoresis (2-DE). 2-DE was carried out with an immobilized pH gradient bar in the first dimension, and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. Over one thousand protein spots were visualized by silver staining and quantified by image processing. In the analyses, 58 protein spots were distinguishable among the above five brain regions, and 17 proteins were shown to be varied in quantity in the course of aging. Partial amino-terminal sequences and/or internal sequences for a total of 301 protein spots were analyzed. One hundred and eighty proteins appeared to have blocked N-termini and 122 proteins were identified. Twenty-seven new proteins were identified by sequence homology search. A mouse brain proteome database was constructed, which consists of the 2-DE map images and the respective spot data files with 15 related references.

Acrylic Resins↗
PubMed2025

Network pharmacology and molecular docking to explore the active compounds and mechanisms of Jerusalem artichoke for treating diabetes.

The effective components and mechanism of Jerusalem artichokes (JAs) in lowering blood glucose were studied through network pharmacology and molecular docking. The active compounds of Jerusalem artichoke were obtained by referring to the literature, and the active compounds were screened. The targets were predicted by the SwissTargetPrediction database, and the disease targets were screened using GeneCard, Disgenet, and OMIM databases. The protein-protein interaction (PPI) network diagram was constructed using the STRING database, and the intersection target was analyzed by gene ontology (GO) biological function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using the David database. Finally, molecular docking was verified using AutoDockTools1.5.7 software. After screening, 412 gene targets, 476 disease targets, and 64 intersection targets were identified. The results of GO biological function analysis and KEGG pathway analysis showed that the technology was involved in multiple biological processes and regulatory pathways for hypoglycemia, such as the HIF-1, PI3K-Akt, and AMPK signaling pathways. Molecular docking results showed that Jasmonate, Liquiritigenin and Inulin of JAs had strong binding effects with PPARG and STAT3. JAs exert hypoglycemic effects through multi-component, multi-target and multi-pathway. In summary, this study investigated the hypoglycemic mechanism of JAs using network pharmacology and molecular interconnection technology, and concluded that JAs exert hypoglycemic effects through multiple components, targets, and pathways, which provides a theoretical basis for the study of JAs.

Molecular Docking Simulation↗
PubMed2006

Computational protein design: a novel path to future protein drugs.

Computational protein design emerges in recent years as a field that could make a substantial impact on the design of protein drugs. It still consists mainly of redesigning parts of a protein sequence for increasing the stability of a given 3-dimensional conformation of a protein, but has already been extended from redesigning core residues to redesigning in all other protein regions, as well as to the design of backbone conformations. More recently, proteins with new binding functions and new enzymes, protein libraries, designs of full folds and of a new protein fold, have been some of the main highlights. The search and the scoring problems are however not fully solved, and many of the design processes should be examined on much larger scales in order to assess their usefulness. We examine some of the basic assumptions in computational protein design, in particular, the separation between sequence and scaffold designs. Among others, we suggest to include more protein residues in computations, to include relevant parts of the backbone, to use appropriate reference states, to produce the proteins and to validate the designs by structural examination of the protein products.

Computational Biology↗
PubMed2004

A database of [(18)F]-altanserin binding to 5-HT(2A) receptors in normal volunteers: normative data and relationship to physiological and demographic variables.

This study presents the results of an analysis of 5-hydroxytryptamine (5-HT)(2A) receptors in 52 healthy subjects. Thirty men and twenty-two women aged between 21 and 79 years were investigated with magnetic resonance imaging (MRI) and [(18)F]-altanserin positron emission tomography (PET). The distribution volumes of specific tracer binding (DV(3)') was calculated for 15 brain regions using either cerebellum or pons as reference regions and correlations between DV(3)' and physiological and demographic variables were made. The regional distribution of [(18)F]-altanserin binding in the healthy human brain was in agreement with existing in vitro post-mortem human 5-HT(2A) data. Apart from nonspecific cerebellar binding (DV(2)), there was no gender difference in 5-HT(2A) binding. A positive correlation between cerebellar binding and age was observed and negative correlations between age and DV(3)' were found in all cortical regions, except occipital cortex, corresponding to a decrease in DV(3)' of 6% or 4% per decade with cerebellum or pons as reference regions, respectively. In several temporal and frontal cortical regions, positive correlations were found between body mass index (BMI) and DV(3)'. Our findings provide a resource to aid design of clinical studies of the 5-HT(2A) receptors. [(18)F]-altanserin binding appears to be unaffected by gender, but the effects of ageing must be considered for clinical studies. The correlations between different cortical regions' 5-HT(2A) binding and BMI should be explored in future studies.

Adult↗
PubMed2003

Normal human dermal fibroblasts: proteomic analysis of cell layer and culture medium.

Proteins present within the cell layer and those released in the cell medium from in vitro cultured normal human dermal fibroblasts were separated and characterized in terms of their isoelectric point and molecular weight, by two-dimensional (2-D) gel electrophoresis. All spots in the synthetic gel were firstly analyzed by the Melanie 3 software and compared with those of breast cancer cells, colorectal epithelial cells, HL60, lymphoma cells, and platelets, already available on-line. From the identification of 144 spots from both the cell layer and the medium, we were able to recognize 89 different proteins, since a certain number of spots represented different isoforms of the same molecule. Identifications were performed by matching with on-line 2-D databases, and by matrix assisted laser-desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS), in order to confirm the identification by matching, or to identify new proteins. The procedure we used allows (i) to design a highly reproducible reference map of the proteome of adult human normal fibroblasts in culture, (ii) to evaluate protein species produced in the cell layer as well as those released in the culture medium, and (iii) to compare data from gel matching with those obtained by MS. This work represents an essential step for a better knowledge of mesenchymal cells, given the widespread use of this cell type in both clinical and experimental investigations.

Adult↗
PubMed2004

COMe: the ontology of bioinorganic proteins.

BACKGROUND: Many characterised proteins contain metal ions, small organic molecules or modified residues. In contrast, the huge amount of data generated by genome projects consists exclusively of sequences with almost no annotation. One of the goals of the structural genomics initiative is to provide representative three-dimensional (3-D) structures for as many protein/domain folds as possible to allow successful homology modelling. However, important functional features such as metal co-ordination or a type of prosthetic group are not always conserved in homologous proteins. So far, the problem of correct annotation of bioinorganic proteins has been largely ignored by the bioinformatics community and information on bioinorganic centres obtained by methods other than crystallography or NMR is only available in literature databases. RESULTS: COMe (Co-Ordination of Metals) represents the ontology for bioinorganic and other small molecule centres in complex proteins. COMe consists of three types of entities: 'bioinorganic motif' (BIM), 'molecule' (MOL), and 'complex proteins' (PRX), with each entity being assigned a unique identifier. A BIM consists of at least one centre (metal atom, inorganic cluster, organic molecule) and two or more endogenous and/or exogenous ligands. BIMs are represented as one-dimensional (1-D) strings and 2-D diagrams. A MOL entity represents a 'small molecule' which, when in complex with one or more polypeptides, forms a functional protein. The PRX entities refer to the functional proteins as well as to separate protein domains and subunits. The complex proteins in COMe are subdivided into three categories: (i) metalloproteins, (ii) organic prosthetic group proteins and (iii) modified amino acid proteins. The data are currently stored in both XML format and a relational database and are available at http://www.ebi.ac.uk/come/. CONCLUSION: COMe provides the classification of proteins according to their 'bioinorganic' features and thus is orthogonal to other classification schemes, such as those based on sequence similarity, 3-D fold, enzyme activity, or biological process. The hierarchical organisation of the controlled vocabulary allows both for annotation and querying at different levels of granularity.

Binding Sites↗
PubMed2004

Requirement of hydD, hydE, hypC and hypE genes for hydrogenase activity in Helicobacter pylori.

Helicobacter pylori possesses a membrane-bound, nickel containing, hydrogen uptake hydrogenase enzyme; its synthesis requires structural as well as accessory proteins, the latter needed for the complete maturation of the enzyme. Our lab previously characterized mutants in the accessory hyp genes, hypA, hypB, hypD and hypF that were all severely affected for hydrogenase activity, and in some cases (hypA and hypB mutants) also affected for urease activity. This finding prompted us to disrupt the two remaining unstudied hyp genes of H. pylori, hypC and hypE, in order to see if the same pleiotropic effect would be observed. In both mutants hydrogenase activity was abolished but urease activity remained unaffected. Addition of 5 microM nickel into the growth medium partially restored the hydrogenase activity in the hypE mutant and to a lesser extent in the hypC mutant. In addition, we also disrupted the genes HP0634 (referred as hydD in the H. pylori 26695 genome database) and HP0635 (whose function was unknown, referred to here as hydE) to address their possible roles in the hydrogenase synthesis/maturation process. In both cases, hydrogenase activities were abolished and addition of nickel could not restore the activity, suggesting that these proteins are involved in the hydrogenase synthesis process rather than in nickel mobilization/insertion steps.

Bacterial Proteins↗
PubMed2004

PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms.

BACKGROUND: The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups (COGs). There are several bioinformatic studies that made use of this database to determine (hyper)thermophile-specific proteins by searching for COGs containing (almost) exclusively proteins from (hyper)thermophilic genomes. However, public software to perform individually definable group-specific searches is not available. RESULTS: The tool described here exactly fills this gap. The software is accessible at http://www.uni-wh.de/pcogr and is linked to the COG-database. The user can freely define two groups of organisms by selecting for each of the (current) 66 organisms to belong either to groupA, to the reference groupB or to be ignored by the algorithm. Then, for all COGs a specificity index is calculated with respect to the specificity to groupA, i. e. high scoring COGs contain proteins from the most of groupA organisms while proteins from the most organisms assigned to groupB are absent. In addition to ranking all COGs according to the user defined specificity criteria, a graphical visualization shows the distribution of all COGs by displaying their abundance as a function of their specificity indexes. CONCLUSIONS: This software allows detecting COGs specific to a predefined group of organisms. All COGs are ranked in the order of their specificity and a graphical visualization allows recognizing (i) the presence and abundance of such COGs and (ii) the phylogenetic relationship between groupA- and groupB-organisms. The software also allows detecting putative protein-protein interactions, novel enzymes involved in only partially known biochemical pathways, and alternate enzymes originated by convergent evolution.

Escherichia coli↗
PubMed2000

Analysis of knowledge-based protein-ligand potentials using a self-consistent method.

We propose a self-consistent approach to analyze knowledge-based atom-atom potentials used to calculate protein-ligand binding energies. Ligands complexed to actual protein structures were first built using the SMoG growth procedure (DeWitte & Shakhnovich, 1996) with a chosen input potential. These model protein-ligand complexes were used to construct databases from which knowledge-based protein-ligand potentials were derived. We then tested several different modifications to such potentials and evaluated their performance on their ability to reconstruct the input potential using the statistical information available from a database composed of model complexes. Our data indicate that the most significant improvement resulted from properly accounting for the following key issues when estimating the reference state: (1) the presence of significant nonenergetic effects that influence the contact frequencies and (2) the presence of correlations in contact patterns due to chemical structure. The most successful procedure was applied to derive an atom-atom potential for real protein-ligand complexes. Despite the simplicity of the model (pairwise contact potential with a single interaction distance), the derived binding free energies showed a statistically significant correlation (approximately 0.65) with experimental binding scores for a diverse set of complexes.

Ligands↗
PubMed2003

Disease genes and intracellular protein networks.

By a computational approach we reconstructed genomic transcriptional profiles of 19 different adult human tissues, based on information on activity of 27,924 genes obtained from unbiased UniGene cDNA libraries. In each considered tissue, a small number of genes resulted highly expressed or "tissue specific." Distribution of gene expression levels in a tissue appears to follow a power law, thus suggesting a correspondence between transcriptional profile and "scale-free" topology of protein networks. The expression of 737 genes involved in Mendelian diseases was analyzed, compared with a large reference set of known human genes. Disease genes resulted significantly more expressed than expected. The possible correspondence of their products to important nodes of intracellular protein network is suggested. Auto-organization of the protein network, its stability in time in the differentiated state, and relationships with the degree of genetic variability at genome level are discussed.

Adult↗
PubMed2006

Monomorphism of human cytochrome c.

Cytochrome c (Cyt c) has key roles in both mitochondrial electron transfer and apoptosis onset and is therefore likely undergoing a strong selective pressure against amino acid variation. Nevertheless, a phylogenetically fast amino acid replacement rate in the Cyt c of species of the anthropoid primate lineage was recently reported. We therefore looked for the presence of nonsynonymous single nucleotide polymorphisms (nsSNPs) in the human Cyt c (HGNC approved gene symbol: CYCS), which, given its cellular constraints, could have important functional consequences, and found a large number of putative nsSNPs reported in the dbSNP database. We then subjected these putative SNPs to experimental validation by sequencing the Cyt c gene in a panel of 95 individuals assumed as a standard reference of the human population diversity. Surprisingly, none of the putative SNPs survived experimental validation. We conclude that non-rare allelic variants of the Cyt c protein are absent in the human populations analyzed in this study.

Alleles↗
PubMed2001

BioMolQuest: integrated database-based retrieval of protein structural and functional information.

MOTIVATION: Information about a particular protein or protein family is usually distributed among multiple databases and often in more than one entry in each database. Retrieval and organization of this information can be a laborious task. This task is complicated even further by the existence of alternative terms for the same concept. RESULTS: The PDB, SWISS-PROT, ENZYME, and CATH databases have been imported into a combined relational database, BIOMOLQUEST: A powerful search engine has been built using this database as a back end. The search engine achieves significant improvements in query performance by automatically utilizing cross-references between the legacy databases. The results of the queries are presented in an organized, hierarchical way.

Abstracting and Indexing↗
PubMed2005

Get ready to GO! A biologist's guide to the Gene Ontology.

The Gene Ontology (GO) project provides a controlled vocabulary to facilitate high-quality functional gene annotation for all species. Genes in biological databases are linked to GO terms, allowing biologists to ask questions about gene function in a manner independent of species. This tutorial provides an introduction for biologists to the GO resources and covers three of the most common methods of querying GO: by individual gene, by gene function and by using a list of genes. [For the sake of brevity, the term 'gene' is used throughout this paper to refer to genes and their products (proteins and RNAs). GO annotations are always based on the characteristics of gene products, even though it may be the gene that is cited in the annotation.].

Abstracting and Indexing↗
PubMed1996

Structural analysis and identification of gel-purified proteins, available in the femtomole range, using a novel computer program for peptide sequence assignment, by matrix-assisted laser desorption ionization-reflectron time-of-flight-mass spectrometry.

A procedure is described for structural characterization and identification of proteins, purified by either one- or two-dimensional gel electrophoresis in the low picomole to femtomole range. The purified proteins are first detected in the primary gels by the sensitive reverse staining procedure described by Fernandez-Patron et al. (Anal. Biochem. 1995, 224, 203-211) and consecutively reeluted from combined get pieces and concentrated in the tip of a Pasteur pipette in a secondary gel matrix consisting of either sodium dodecyl sulfate-polyacrylamide or agarose. The concentrated proteins are in-matrix-digested and the resulting peptides are separated by reverse-phase high performance liquid chromatography (HPLC) combined with microsequencing or analyzed by matrix-assisted laser desorption ionization--time of flight--mass spectrometry. Protein identification is based on sequence homology or on the peptide mass pattern. The matching peptide sequences can additionally be verified by matching their measured post-source decay spectra with the calculated fragmentation patterns of the isobaric candidate peptides appearing on the search list. This is done by a computer program referred to as MassFrag, described in this paper. We demonstrate that it is possible to identify protein that are only available in the femtomole range and whose sequences are stored in nonredundant protein databases or nucleotide and expressed sequence tag databases.

Amino Acid Sequence↗
PubMed2002

A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics.

The chemical shift difference (delta[13C(beta)]-delta[13C(gamma)]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1,033 prolines from 304 proteins deposited in the BioMagRes database, a software tool was created to predict the probabilities for cis or trans conformations of Xaa-Pro peptide bonds. Using this approach, the conformation at a given Xaa-Pro bond can be identified in a simple NOE-independent way immediately after obtaining its NMR resonance assignments. This will allow subsequent structure calculations to be initiated using the correct polypeptide chain conformation.

Amino Acids↗