Dataset Information

Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics.

ABSTRACT: The Proteome Division of Incyte Genomics has released new volumes to the BioKnowledge Library to add human, mouse and rat protein information to its rich collection of model organism Proteome Databases. The Human Proteome Survey Database (HumanPSD) compiles the fundamental properties of more than 25 000 characterized mammalian proteins. HumanPSD includes clear, concise and current protein descriptions (Title Lines), the protein sequence, calculated physical properties, precomputed BLAST alignments, controlled-vocabulary protein properties and Gene Ontology terms, and a list of published references. Each report also contains expression data, Pfam domain information and an associated Mouse Mutant Phenotype section describing behavioral, physiological and cellular phenotypes for over 1500 mouse mutant phenotypes. GPCR-PD contains more than 3200 Protein Reports from the three mammalian species for G protein-coupled receptors, their protein ligands, associated G-proteins and their downstream signaling proteins. In addition to the features described above, each GPCR-PD Protein Report displays annotations of experimental findings from over 10 000 publications. These databases provide important new volumes of Proteome's BioKnowledge Library (http://www.incyte.com), integrating protein information from model organisms with the human proteome.

SUBMITTER: Hodges PE

PROVIDER: S-EPMC99168 | biostudies-literature | 2002 Jan

REPOSITORIES: biostudies-literature

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Publications

Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics.

Hodges Peter E PE Carrico Pauline M PM Hogan Jennifer D JD O'Neill Kathy E KE Owen J J JJ Mangan Mary M Davis Brian P BP Brooks Joan E JE Garrels James I JI

Nucleic acids research 20020101 1

The Proteome Division of Incyte Genomics has released new volumes to the BioKnowledge Library to add human, mouse and rat protein information to its rich collection of model organism Proteome Databases. The Human Proteome Survey Database (HumanPSD) compiles the fundamental properties of more than 25 000 characterized mammalian proteins. HumanPSD includes clear, concise and current protein descriptions (Title Lines), the protein sequence, calculated physical properties, precomputed BLAST alignmen ...[more]

PMID: 11752275

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Project description:G protein-coupled receptors (GPCRs) constitute the largest group of membrane receptor proteins in eukaryotes. Due to their significant roles in various physiological processes such as vision, smell and inflammation, GPCRs are the targets of many prescription drugs. However, the functional and sequence diversity of GPCRs has kept their prediction and classification based on amino acid sequence data as a challenging bioinformatics problem. There are existing computational approaches, mainly using machine learning and statistical methods, to predict and classify GPCRs based on amino acid sequence and sequence derived features. In this paper, we describe a searchable MySQL database, named GPCR-PEnDB (GPCR Prediction Ensemble Database), of confirmed GPCRs and non-GPCRs. It was constructed with the goal of allowing users to conveniently access useful information of GPCRs in a wide range of organisms and to compile reliable training and testing datasets for different combinations of computational tools. This database currently contains 3129 confirmed GPCR and 3575 non-GPCR sequences collected from the UniProtKB/Swiss-Prot protein database, encompassing over 1200 species. The non-GPCR entries include transmembrane proteins for evaluating various prediction programs' abilities to distinguish GPCRs from other transmembrane proteins. Each protein is linked to information about its source organism, classification, sequence lengths and composition, and other derived sequence features. We present examples of using this database along with its graphical user interface, to query for GPCRs with specific sequence properties and to compare the accuracies of five tools for GPCR prediction. This initial version of GPCR-PEnDB will provide a framework for future extensions to include additional sequence and feature data to facilitate the design and assessment of software tools and experimental studies to help understand the functional roles of GPCRs. Database URL: gpcr.utep.edu/database.

Project description:In the nasal cavity, the nonmotile cilium of olfactory sensory neurons (OSNs) constitutes the chemosensory interface between the ambient environment and the brain. The unique sensory organelle facilitates odor detection for which it includes all necessary components of initial and downstream olfactory signal transduction. In addition to its function in olfaction, a more universal role in modulating different signaling pathways is implicated, for example, in neurogenesis, apoptosis, and neural regeneration. To further extend our knowledge about this multifunctional signaling organelle, it is of high importance to establish a most detailed proteome map of the ciliary membrane compartment down to the level of transmembrane receptors. We detached cilia from mouse olfactory epithelia via Ca(2+)/K(+) shock followed by the enrichment of ciliary membrane proteins at alkaline pH, and we identified a total of 4,403 proteins by gel-based and gel-free methods in conjunction with high resolution LC/MS. This study is the first to report the detection of 62 native olfactory receptor proteins and to provide evidence for their heterogeneous expression at the protein level. Quantitative data evaluation revealed four ciliary membrane-associated candidate proteins (the annexins ANXA1, ANXA2, ANXA5, and S100A5) with a suggested function in the regulation of olfactory signal transduction, and their presence in ciliary structures was confirmed by immunohistochemistry. Moreover, we corroborated the ciliary localization of the potassium-dependent Na(+)/Ca(2+) exchanger (NCKX) 4 and the plasma membrane Ca(2+)-ATPase 1 (PMCA1) involved in olfactory signal termination, and we detected for the first time NCKX2 in olfactory cilia. Through comparison with transcriptome data specific for mature, ciliated OSNs, we finally delineated the membrane ciliome of OSNs. The membrane proteome of olfactory cilia established here is the most complete today, thus allowing us to pave new avenues for the study of diverse molecular functions and signaling pathways in and out of olfactory cilia and thus to advance our understanding of the biology of sensory organelles in general.

Project description:BACKGROUND: G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. DESCRIPTION: Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. CONCLUSIONS: The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs. The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.

Dataset Information

Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics.

Publications

Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics.

Similar Datasets

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