InterPro in 2011: New developments in the family and domain prediction database

EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK.
Nucleic Acids Research (Impact Factor: 9.11). 11/2011; 40(Database issue):D306-12. DOI: 10.1093/nar/gkr948
Source: PubMed


InterPro ( is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely
available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures,
against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale
analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview
of new developments in the database and its associated software since 2009, including updates to database content, curation
processes and Web and programmatic interfaces.

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    • "S. boliviensis redox-related proteins identified in combined Pv-Proteomes 1 and 2 include 5 thioredoxin-related proteins, 5 peroxiredoxin-related proteins, 2 glutaredoxins, 5 glutathione-related metabolic enzymes, 2 superoxide dismutases and catalase. Identified P. vivax redox-related proteins include a 2 peroxiredoxins, 2 glutaredoxins, thioredoxin, superoxide dismutase, glutathione reductase, and merozoite capping protein 1, and a putative thiol peroxidase protecting cells against reactive oxygen species toxicity [54]. The most abundant P. vivax and S. boliviensis proteins as calculated by Mascot [43] using the exponentially multiplied protein abundance index (emPAI, [55]) are listed in Supplemental Table 3. "
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    ABSTRACT: Unlabelled: Plasmodium vivax is the causative infectious agent of 80-300 million annual cases of malaria. Many aspects of this parasite's biology remain unknown. To further elucidate the interaction of P. vivax with its Saimiri boliviensis host, we obtained detailed proteomes of infected red blood cells, representing the trophozoite-enriched stage of development. Data from two of three biological replicate proteomes, emphasized here, were analyzed using five search engines, which enhanced identifications and resulted in the most comprehensive P. vivax proteomes to date, with 1375 P. vivax and 3209 S. boliviensis identified proteins. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with P. vivax's known reticulocyte host-cell specificity. A majority of the host and pathogen proteins identified belong to specific functional categories, and several parasite gene families, while 33% of the P. vivax proteins have no reported function. Hemoglobin was significantly oxidized in both proteomes, and additional protein oxidation and nitration was detected in one of the two proteomes. Detailed analyses of these post-translational modifications are presented. The proteins identified here significantly expand the known P. vivax proteome and complexity of available host protein functionality underlying the host-parasite interactive biology, and reveal unsuspected oxidative modifications that may impact protein function. Biological significance: Plasmodium vivax malaria is a serious neglected disease, causing an estimated 80 to 300 million cases annually in 95 countries. Infection can result in significant morbidity and possible death. P. vivax, unlike the much better-studied Plasmodium falciparum species, cannot be grown in long-term culture, has a dormant form in the liver called the hypnozoite stage, has a reticulocyte host-cell preference in the blood, and creates caveolae vesicle complexes at the surface of the infected reticulocyte membranes. Studies of stage-specific P. vivax expressed proteomes have been limited in scope and focused mainly on pathogen proteins, thus limiting understanding of the biology of this pathogen and its host interactions. Here three P. vivax proteomes are reported from biological replicates based on purified trophozoite-infected reticulocytes from different Saimiri boliviensis infections (the main non-human primate experimental model for P. vivax biology and pathogenesis). An in-depth analysis of two of the proteomes using 2D LC/MS/MS and multiple search engines identified 1375 pathogen proteins and 3209 host proteins. Numerous functional categories of both host and pathogen proteins were identified, including several known P. vivax protein family members (e.g., PHIST, eTRAMP and VIR), and 33% of protein identifications were classified as hypothetical. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with this parasite species' known reticulocyte host-cell specificity. In two biological replicates analyzed for post-translational modifications, hemoglobin was extensively oxidized, and various other proteins were also oxidized or nitrated in one of the two replicates. The cause of such protein modification remains to be determined but could include oxidized heme and oxygen radicals released from the infected red blood cell's parasite-induced acidic digestive vacuoles. In any case, the data suggests the presence of distinct infection-specific conditions whereby both the pathogen and host infected red blood cell proteins may be subject to significant oxidative stress.
    Journal of Proteomics 12/2014; 115. DOI:10.1016/j.jprot.2014.12.010 · 3.89 Impact Factor
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    • "This ORF (SAR2008 of the MRSA252 genome, herein referred to as pdt) encodes a predicted prephenate dehydratase (saPDT) enzyme, which catalyzes the formation of phenylpyruvate from prephenate during phenylalanine biosynthesis [23]. A conserved domain search [37] of the S. aureus pdt ORF revealed the presence of signature catalytic (PDT; IPR001086) and regulatory (ACT; IPR002912) domains present in mono-functional PDT enzymes that are common to Gram-positive bacteria [23]. A BLAST search [38] using the S. aureus MRSA252 nucleotide sequence spanning the nos and pdt ORFs revealed that this organization is present in all sequenced S. aureus genomes, as well as all sequenced coagulase-negative staphylococcal genomes currently available in the National Center for Biotechnology Information (NCBI) genome database (Fig. 1). "
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    ABSTRACT: Nitric oxide (NO) is emerging as an important regulator of bacterial stress resistance, biofilm development, and virulence. One potential source of endogenous NO production in the pathogen Staphylococcus aureus is its NO-synthase (saNOS) enzyme, encoded by the nos gene. Although a role for saNOS in oxidative stress resistance, antibiotic resistance, and virulence has been recently-described, insights into the regulation of nos expression and saNOS enzyme activity remain elusive. To this end, transcriptional analysis of the nos gene in S. aureus strain UAMS-1 was performed, which revealed that nos expression increases during low-oxygen growth and is growth-phase dependent. Furthermore, nos is co-transcribed with a downstream gene, designated pdt, which encodes a prephenate dehydratase (PDT) enzyme involved in phenylalanine biosynthesis. Deletion of pdt significantly impaired the ability of UAMS-1 to grow in chemically-defined media lacking phenylalanine, confirming the function of this enzyme. Bioinformatics analysis revealed that the operon organization of nos-pdt appears to be unique to the staphylococci. As described for other S. aureus nos mutants, inactivation of nos in UAMS-1 conferred sensitivity to oxidative stress, while deletion of pdt did not affect this phenotype. The nos mutant also displayed reduced virulence in a murine sepsis infection model, and increased carotenoid pigmentation when cultured on agar plates, both previously-undescribed nos mutant phenotypes. Utilizing the fluorescent stain 4-Amino-5-Methylamino-2',7'-Difluorofluorescein (DAF-FM) diacetate, decreased levels of intracellular NO/reactive nitrogen species (RNS) were detected in the nos mutant on agar plates. These results reinforce the important role of saNOS in S. aureus physiology and virulence, and have identified an in vitro growth condition under which saNOS activity appears to be upregulated. However, the significance of the operon organization of nos-pdt and potential relationship between these two enzymes remains to be elucidated.
    PLoS ONE 10/2014; 9(10):e108868. DOI:10.1371/journal.pone.0108868 · 3.23 Impact Factor
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    • "The motifs were validated using ScanProsite tool (De Castro et al., 2006) by scanning against UniProtKB/TrEMBL databases (release 2014_01) (Boeckmann et al., 2003). From the ScanProsite results, corresponding UniProt protein entries matching the motif were retrieved and their Pfam (Punta et al., 2012) domain and InterPro (Hunter et al., 2012) domain annotation noted. Linear and discontinuous epitopes were predicted using ElliPro server (Ponomarenko et al., 2008). "
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    ABSTRACT: Adhesion of uropathogenic E. coli (UPEC) to uroepithelial cell receptors is facilitated through the lectin domain of FimH adhesin. In the current study, Molecular Dynamics (MD) simulations were performed for the lectin domain of FimH from UPEC J96. The high affinity state lectin domain was found to be stable and rigid during the simulations. Further, based on conserved subsequences around one of the disulfide forming cysteines, two sequence motifs were designed. An immunoinformatics approach was utilized to identify linear and discontinuous epitopes for the lectin domain of FimH. We propose that the accessibility of predicted epitopes should also be assessed in a dynamic aqueous environment to evaluate the potential of vaccine candidates. Since MD simulation data enables assessing the accessibility in a dynamic environment, we evaluated the accessibility of the top ranked discontinuous and linear epitopes using structures obtained at every nanosecond (ns) in the 1-20ns MD simulation timeframe. Knowledge gained in this study has a potential utility in the design of vaccine candidates for Urinary Tract Infection (UTI).
    Computational Biology and Chemistry 10/2014; 52:18–24. DOI:10.1016/j.compbiolchem.2014.08.002 · 1.12 Impact Factor
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