Pubget: learning materials for Computational Biology

We present an application of in silico quantitative structure-activity relationship (QSAR) models to establish a new ligand-based computational approach for generating virtual libraries. The Free-Wilson methodology was applied to extract rules from two data sets containing compounds which were scree... | PMID: 20981520

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Audio, Transactions of the IRE Professional Group on (286)38 2011

The five near-iron transporter (NEAT) domain anthrax hemophore, IsdX2, scavenges heme from hemoglobin and transfers heme to the surface protein IsdC.

Erin Sarah ES Honsa, Marian M Fabian, Ana Maria AM Cardenas, John S JS Olson and Anthony William AW Maresso

Abstract

We purified each individual NEAT domain of IsdX2 as a GST fusion and analyzed the specific function of each domain as it relates to heme acquisition and transport. NEAT domains 1, 3, 4, and 5 all bind heme, with domain 5 having the highest affinity. All NEATs associate with hemoglobin, but only NEAT... | PMID: 21808055

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Biochimica et Biophysica Acta (1814)9 2011

Characterization of the single-stranded DNA binding protein pV(VGJPhi) of VGJPhi phage from Vibrio cholerae.

Alina A Falero, Andy A Caballero, Sonia S Trigueros, Celso C Pérez, Javier J Campos, Karen K Marrero and Rafael R Fando

Abstract

We show that this protein has a general affinity for single-stranded DNA (ssDNA) as documented by Electrophoretic Mobility Shift Assay (EMSA). The apparent molecular weight of the monomer is about 12.7kDa as measured by HPLC-SEC. Moreover, isoelectrofocusing showed an isoelectric point for pV(VGJΦ)... | PMID: 21586349

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Biochimica et Biophysica Acta (1814)9 2011

Identification of the phosphorylation sites in the survival motor neuron protein by protein kinase A.

Chia-Yen CY Wu, Amelia A Curtis, Yong Seok YS Choi, Miho M Maeda, Mary Jue MJ Xu, Amanda A Berg, Upasana U Joneja, Robert W RW Mason, Kelvin H KH Lee and Wenlan W Wang

Abstract

The survival motor neuron (SMN) protein plays an essential role in the assembly of uridine-rich small nuclear ribonuclear protein complexes. Phosphorylation of SMN can regulate its function, stability, and sub-cellular localization. This study shows that protein kinase A (PKA) phosph... | PMID: 21609790

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Journal of Computational Biology (18)9 2011

Proceedings of the Satellite Workshop on Comparative Genomics, Research in Computational Molecular Biology (RECOMB-CG). Ottawa, Canada. October 2010.

Author(s) unavailable

Abstract

PMID: 22256359

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Nature Reviews: Genetics (12)9 2011

Understanding the transcriptome through RNA structure.

Yue Wan, Michael Kertesz, Robert C Spitale, Eran Segal and Howard Y Chang

Abstract

RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational pred... | PMID: 21850044

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Systems Biology, IET (5)5 2011

Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae.

P T Monteiro, P J Dias, D Ropers, A L Oliveira, I Sá-Correia, M C Teixeira and A T Freitas

Abstract

Qualitative models allow understanding the relation between the structure and the dynamics of gene regulatory networks. The dynamical properties of these models can be automatically analysed by means of formal verification methods, like model checking. This facilitates the model-vali... | PMID: 22010757

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Audio, Transactions of the IRE Professional Group on (89)2 2011

Microcephaly with simplified gyration, epilepsy, and infantile diabetes linked to inappropriate apoptosis of neural progenitors.

Cathryn J CJ Poulton, Rachel R Schot, Sima Kheradmand SK Kia, Marta M Jones, Frans W FW Verheijen, Hanka H Venselaar, Marie-Claire Y MC de Wit, Esther E de Graaff, Aida M AM Bertoli-Avella and Grazia M S GM Mancini

Abstract

We reported one of these families previously in a paper on Wolcott-Rallison syndrome (WRS). WRS is characterized by increased apoptotic cell death as part of an uncontrolled unfolded protein response. Increased apoptosis has been shown to be a cause of microcephaly in animal models. An autopsy spec... | PMID: 21835305

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Journal of Proteome Research (10)8 2011

Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation.

Kenny Helsens, Petra Van Damme, Sven Degroeve, Lennart Martens, Thomas Arnesen, Joël Vandekerckhove and Kris Gevaert

Abstract

We here isolated N-terminal peptides of a Saccharomyces cerevisiae proteome and analyzed both annotated and alternative TIS. We analyzed this N-terminome of S. cerevisiae which resulted in the identification of 650 unique N-terminal peptides corresponding to database annotated TIS. Furthermore, 56 u... | PMID: 21619078

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Journal of Proteome Research (10)8 2011

Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705.

Kirsi Savijoki, Niina Lietzén, Matti Kankainen, Tapani Alatossava, Kerttu Koskenniemi, Pekka Varmanen and Tuula A Nyman

Abstract

We used GeLC-MS/MS, in which proteins are separated using 1-DE and identified using nanoLC-MS/MS, to generate high-quality protein catalogs. To maximize the number of identifications, all data sets were searched against the target databases using two search engines, Mascot and Paragon. As a result,... | PMID: 21615180

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