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Vlatka Mičetić Stanković, Department of Zoology, Croatian Natural History Museum, 10000 Zagreb, Croatia ... Ivan Lukić, Division for Forest Protection and Game Management, Croatian Forest Research Institute, 10450 Jastrebarsko, Croatia 2 Dr.sc. ...doi:10.31298/sl.143.11-12.2 fatcat:qht2tk5dn5g3tgynum5w2th7k4
Correction for 'Spatiotemporal distribution and speciation of silver nanoparticles in the healing wound' by Marco Roman et al., Analyst, 2020, 145, 6456–6469, DOI: 10.1039/D0AN00607F.doi:10.1039/d1an90083h pmid:34558571 fatcat:yftlj7nzpzfsth53kuse2zeqpe
Increasingly large numbers of proteins require methods for functional annotation. This is typically based on pairwise inference from the homology of either protein sequence or structure. Recently, similarity networks have been presented to leverage both the ability to visualize relationships between proteins and assess the transferability of functional inference. Here we present PANADA, a novel toolkit for the visualization and analysis of protein similarity networks in Cytoscape. Networks candoi:10.1371/journal.pone.0078383 pmid:24265686 pmcid:PMC3827049 fatcat:32qvawdtjngp5onz5of7rgn3ee
more »... e constructed based on pairwise sequence or structural alignments either on a set of proteins or, alternatively, by database search from a single sequence. The Panada web server, executable for download and examples and extensive help files are available at URL: http://protein.bio.unipd.it/panada/.
Few data exist on the ecotoxicological effects of nanosized titanium dioxide (nTiO 2 ) towards marine species with specific reference to bivalve molluscs and their relative life stages. Mytilus galloprovincialis Lamarck was selected to assess the potential adverse effects of nTiO 2 (0e64 mg/L) on its early larval development stages (pre-D shell stage, malformed D-shell stage and normal D-shell stage larvae) considering two exposure scenarios characterised by total darkness (ASTM protocol) anddoi:10.1016/j.marenvres.2013.08.015 pmid:24060384 fatcat:o4tpye5kvnaqnmofyfdorms5ce
more »... tural photoperiod (light/dark). This approach was considered to check the presence of potential effects associated to the photocatalytic properties of nTiO 2 . Parallel experiments were carried on with the bulk reference TiCl 4 . The toxicity of nTiO 2 showed to be mainly related to its "nano" condition and to be influenced by the exposure to light that supported the increase in the number of pre-D shell stage (retarded) larvae compared to the malformed ones especially at the maximum effect concentrations (4 and 8 mg nTiO 2 /L). The non-linear regression toxicity data analysis showed the presence of two EC50 values per exposure scenario: a) EC(50) 1 ¼ 1.23 mg/L (0.00e4.15 mg/L) and EC(50) 2 ¼ 38.56 mg/L (35.64 e41.47 mg/L) for the dark exposure conditions; b) EC(50) 1 ¼ 1.65 mg/L (0.00e4.74 mg/L) and EC(50) 2 ¼ 16.39 mg/L (13.31e19.48 mg/L) for the light/dark exposure conditions. The potential implication of agglomeration and sedimentation phenomena on ecotoxicological data was discussed.
doi:10.3389/fmicb.2014.00227 pmid:24904542 pmcid:PMC4033309 fatcat:caqxk5nrz5binjvytg4tcc4ymy
Acknowledgments: The authors are thankful to Joško Erceg for the assistance in the sample preparation and Dario Mičetić for GISAXS measurements. ... Data Availability Statement: Datasets available at: Mičetić, Maja (2021), "Structural, Optical and Electrical Properties of Al+MoO 3 and Au+MoO 3 Thin Films Prepared by Magnetron Codeposition", Mendeley ...doi:10.3390/ma14040766 pmid:33562010 fatcat:l3we6cbb7fgflaqmorqnxsnvzu
There are many data sources containing overlapping information about Intrinsically Disordered Proteins (IDP). IDPcentral aims to be a registry to aid the discovery of data about proteins known to be intrinsically disordered by aggregating the content from these sources. Traditional ETL approaches for populating IDPcentral require the API and data model of each source to be wrapped and then transformed into a common model. In this paper, we investigate using Bioschemas markup as a mechanism todblp:conf/swat4ls/GrayPAMH22 fatcat:4drvy5pfdzdgpbl7ew2fiu24qa
more »... pulate the IDPcentral registry by constructing the Intrinsically Disordered Protein Knowledge Graph (idp-kg). Bioschemas markup is a machine-readable, lightweight representation of the content of each page in the site that is embedded in the HTML. For any site it is accessible through a HTTP request. We harvest the Bioschemas markup in three IDP sources and show the resulting idp-kg has the same breadth of proteins available as the original sources, and can be used to gain deeper insight into their content by querying them as a single, consolidated knowledge graph.
The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifyingdoi:10.1093/nar/gkaa1058 pmid:33237329 fatcat:fpb77lr37naaxopskkh2rq7s3e
more »... the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users.
Hemocyanin (Hc) is an oxygen carrier protein in which oxygen binding is regulated by allosteric effectors such as H ؉ and L-lactate. Isothermal titration calorimetric measurements showed that L-lactate binds to dodecameric and heterohexameric Hc and to the CaeSS3 homohexamer but not to the CaeSS2 monomer. The binding of lactate caused no change in the optical absorption and x-ray absorption spectra of either oxy-or deoxy-Hc, suggesting that no structural rearrangement of the active sitedoi:10.1074/jbc.m109.076067 pmid:20406810 pmcid:PMC2885213 fatcat:lzrdvbi2ljhavkevyzi4vcvgli
more »... . At pH 6.5, the oxygen binding rate constant k obs obtained by flash photolysis showed a significant increase upon addition of L-lactate, whereas L-lactate addition had little effect at pH 8.3. Lactate binding caused a concentration-dependent shift in the interhexameric distances at pH 6.5 based on small angle x-ray scattering measurements. These results show that L-lactate affects oxygen affinity at pH 6.5 by modulating the global structure of Hc without affecting its binuclear copper center (the active site). In contrast to this, the active site structure of deoxy-Hc is affected by changes in pH (Hirota, S., Kawahara, T., Beltramini, M., Di Muro, P., Magliozzo, R. S., Peisach, J., Powers, L. S., Tanaka, N., Nagao, S., and Bubacco, L. (2008) J. Biol. Chem. 283, 31941-31948). Upon addiction of lactate, the kinetic behavior of oxygen rebinding for Hc was heterogeneous under low oxygen concentrations at pH 6.5 due to changes in the T and R state populations, and the equilibrium was found to shift from the T toward the R state with addition of lactate.
Citation: Spinozzi F, Mariani P, Mičetić I, Ferrero C, Pontoni D, et al. (2012) Quaternary Structure Heterogeneity of Oligomeric Proteins: A SAXS and SANS Study of the Dissociation Products of Octopus ...doi:10.1371/journal.pone.0049644 pmid:23166737 pmcid:PMC3499515 fatcat:hm76w54rwfgjxo7ksuci534b3u
Leucine-rich repeat kinase 1 and 2 (LRRK1 and LRRK2) are large multidomain proteins containing kinase, GTPase and multiple protein-protein interaction domains, but only mutations in LRRK2 are linked to familial Parkinson's disease (PD). Independent studies suggest that LRRK2 exists in the cell as a complex compatible with the size of a dimer. However, whether this complex is truly a homodimer or a heterologous complex formed by monomeric LRRK2 with other proteins has not been definitivelydoi:10.1371/journal.pone.0043472 pmid:22952686 pmcid:PMC3430690 fatcat:hfrdryxk5za4bhludzkl4tdkqi
more »... due to the limitations in obtaining highly pure proteins suitable for structural characterization. Here, we used stable expression of LRRK1 and LRRK2 in HEK293T cell lines to produce recombinant LRRK1 and LRRK2 proteins of greater than 90% purity. Both purified LRRKs are folded, with a predominantly alpha-helical secondary structure and are capable of binding GTP with similar affinity. Furthermore, recombinant LRRK2 exhibits robust autophosphorylation activity, phosphorylation of model peptides in vitro and ATP binding. In contrast, LRRK1 does not display significant autophosphorylation activity and fails to phosphorylate LRRK2 model substrates, although it does bind ATP. Using these biochemically validated proteins, we show that LRRK1 and LRRK2 are capable of forming homodimers as shown by single-particle transmission electron microscopy and immunogold labeling. These LRRK dimers display an elongated conformation with a mean particle size of 145 Å and 175 Å respectively, which is disrupted by addition of 6M guanidinium chloride. Immunogold staining revealed double-labeled particles also in the pathological LRRK2 mutant G2019S and artificial mutants disrupting GTPase and kinase activities, suggesting that point mutations do not hinder the dimeric conformation. Overall, our findings indicate for the first time that purified and active LRRK1 and LRRK2 can form dimers in their full-length conformation.
The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better capture information available in the PDB, such as high temperature residues in X-ray structures and overall conformational diversity. Novel nucleardoi:10.1093/nar/gkx1071 pmid:29136219 pmcid:PMC5753340 fatcat:ctjxsg7edzee7mdg24psbx667u
more »... agnetic resonance chemical shift data provides an additional experimental information layer on conformational dynamics. Predictions have been expanded to provide new types of annotation on backbone rigidity, secondary structure preference and disordered binding regions. MobiDB 3.0 contains information for the complete UniProt protein set and synchronization has been improved by covering all UniParc sequences. An advanced search function allows the creation of a wide array of custom-made datasets for download and further analysis. A large amount of information and cross-links to more specialized databases are intended to make MobiDB the central resource for the scientific community working on protein intrinsic disorder and mobility.
The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classificationdoi:10.1093/nar/gkaa1097 pmid:33237313 fatcat:l7r6wzdo6rcm5k7cbadrttboha
more »... . The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new levels (Clan > Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures.
doi:10.1093/nar/gkw1279 pmid:27965415 pmcid:PMC5210598 fatcat:mtgbidw4wjem7nzhwo2uyqwwte
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflectdoi:10.1093/nar/gkw1056 pmid:27899601 pmcid:PMC5210544 fatcat:b4frkq46bbh5tij5m45ikb5doe
more »... ous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.
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