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      • Record: found
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      TXNDC5, a Newly Discovered Disulfide Isomerase with a Key Role in Cell Physiology and Pathology

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          Abstract

          Thioredoxin domain-containing 5 (TXNDC5) is a member of the protein disulfide isomerase family, acting as a chaperone of endoplasmic reticulum under not fully characterized conditions As a result, TXNDC5 interacts with many cell proteins, contributing to their proper folding and correct formation of disulfide bonds through its thioredoxin domains. Moreover, it can also work as an electron transfer reaction, recovering the functional isoform of other protein disulfide isomerases, replacing reduced glutathione in its role. Finally, it also acts as a cellular adapter, interacting with the N-terminal domain of adiponectin receptor. As can be inferred from all these functions, TXNDC5 plays an important role in cell physiology; therefore, dysregulation of its expression is associated with oxidative stress, cell ageing and a large range of pathologies such as arthritis, cancer, diabetes, neurodegenerative diseases, vitiligo and virus infections. Its implication in all these important diseases has made TXNDC5 a susceptible biomarker or even a potential pharmacological target.

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          CSS-Palm 2.0: an updated software for palmitoylation sites prediction.

          Jian Ren, Longping Wen, Xinjiao Gao … (2008)
          Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm.
          Article 0 comments Cited 214 times – based on 0 reviews     Review now
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            GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs

            Qi Zhao, Yubin Xie, Yueyuan Zheng … (2014)
            Small ubiquitin-like modifiers (SUMOs) regulate a variety of cellular processes through two distinct mechanisms, including covalent sumoylation and non-covalent SUMO interaction. The complexity of SUMO regulations has greatly hampered the large-scale identification of SUMO substrates or interaction partners on a proteome-wide level. In this work, we developed a new tool called GPS-SUMO for the prediction of both sumoylation sites and SUMO-interaction motifs (SIMs) in proteins. To obtain an accurate performance, a new generation group-based prediction system (GPS) algorithm integrated with Particle Swarm Optimization approach was applied. By critical evaluation and comparison, GPS-SUMO was demonstrated to be substantially superior against other existing tools and methods. With the help of GPS-SUMO, it is now possible to further investigate the relationship between sumoylation and SUMO interaction processes. A web service of GPS-SUMO was implemented in PHP + JavaScript and freely available at http://sumosp.biocuckoo.org.
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              PHOSIDA 2011: the posttranslational modification database

              Florian Gnad, Jeremy Gunawardena, Matthias Mann (2010)
              The primary purpose of PHOSIDA (http://www.phosida.com) is to manage posttranslational modification sites of various species ranging from bacteria to human. Since its last report, PHOSIDA has grown significantly in size and evolved in scope. It comprises more than 80 000 phosphorylated, N-glycosylated or acetylated sites from nine different species. All sites are obtained from high-resolution mass spectrometric data using the same stringent quality criteria. One of the main distinguishing features of PHOSIDA is the provision of a wide range of analysis tools. PHOSIDA is comprised of three main components: the database environment, the prediction platform and the toolkit section. The database environment integrates and combines high-resolution proteomic data with multiple annotations. High-accuracy species-specific phosphorylation and acetylation site predictors, trained on the modification sites contained in PHOSIDA, allow the in silico determination of modified sites on any protein on the basis of the primary sequence. The toolkit section contains methods that search for sequence motif matches or identify de novo consensus, sequences from large scale data sets.
              Article 0 comments Cited 151 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Johannes Haybaeck: Role: External Editor
                Journal
                Journal ID (nlm-ta): Int J Mol Sci
                Journal ID (iso-abbrev): Int J Mol Sci
                Journal ID (publisher-id): ijms
                Title: International Journal of Molecular Sciences
                Publisher: MDPI
                ISSN (Electronic): 1422-0067
                Publication date (Electronic): 17 December 2014
                Publication date Collection: December 2014
                Volume: 15
                Issue: 12
                Pages: 23501-23518
                Affiliations
                [1 ]Grado de Biotecnología, Universidad de Zaragoza, Zaragoza E-50013, Spain; E-Mails: elenahornaterron@ 123456gmail.com (E.H.-T.); albertopradilladieste@ 123456gmail.com (A.P.-D.); csanchezdg@ 123456gmail.com (C.S.-D.)
                [2 ]Departamento Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón (IIS), Universidad de Zaragoza, Zaragoza E-50013, Spain
                [3 ]CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid E-28029, Spain
                Author notes
                [* ]Author to whom correspondence should be addressed; E-Mail: josada@ 123456unizar.es ; Tel.: +34-976-761-644; Fax: +34-976-761-612.
                Article
                Publisher ID: ijms-15-23501
                DOI: 10.3390/ijms151223501
                PMC ID: 4284777
                PubMed ID: 25526565
                SO-VID: a7c2d916-18b5-4693-a072-abbb19782e96
                Copyright © © 2014 by the authors; licensee MDPI, Basel, Switzerland.
                License:

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 16 September 2014
                Date revision received : 01 December 2014
                Date accepted : 05 December 2014
                Categories
                Subject: Review

                ScienceOpen disciplines: Molecular biology
                Keywords: thioredoxin domain containing 5 (txndc5),protein disulfide isomerase (pdi),endoplasmic reticulum 46 (erp46),pdi15,thioredoxin-related protein in the cell plasma (pc-trp),endo pdi
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: thioredoxin domain containing 5 (txndc5), protein disulfide isomerase (pdi), endoplasmic reticulum 46 (erp46), pdi15, thioredoxin-related protein in the cell plasma (pc-trp), endo pdi

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