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Bjornson KP Blackwell LJ Sage H Baitinger C Allen D Modrich P 《The Journal of biological chemistry》2003,278(36):34667-34673
Analytical equilibrium ultracentrifugation indicates that Escherichia coli MutS exists as an equilibrating mixture of dimers and tetramers. The association constant for the dimer-to-tetramer transition is 2.1 x 10(7) M-1, indicating that the protein would consist of both dimers and tetramers at physiological concentrations. The carboxyl terminus of MutS is required for tetramer assembly because a previously described 53-amino acid carboxyl-terminal truncation (MutS800) forms a limiting species of a dimer (Obmolova, G., Ban, C., Hsieh, P., and Yang, W. (2000) Nature 407, 703-710; Lamers, M. H., Perrakis, A., Enzlin, J. H., Winterwerp, H. H., de Wind, N., and Sixma, T. K. (2000) Nature 407, 711-717). MutS800 binds a 20-base pair heteroduplex an order of magnitude more weakly than full-length MutS, and at saturating protein concentrations, the heteroduplex-bound mass observed with MutS800 is only half that observed with the full length protein, indicating that the subunit copy number of heteroduplex-bound MutS is twice that of MutS800. Analytical equilibrium ultracentrifugation using a fluorescein-tagged 20-base pair heteroduplex demonstrated that native MutS forms a tetramer on this single site-sized heteroduplex DNA. Equilibrium fluorescence experiments indicated that dimer-to-tetramer assembly promotes mismatch binding by MutS and that the tetramer can bind only a single heteroduplex molecule, implying nonequivalence of the two dimers within the tetramer. Compared with native MutS, the ability of MutS800 to promote MutL-dependent activation of MutH is substantially reduced. 相似文献
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YPED:An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research
Christopher M.Colangelo Mark Shifman Kei-Hoi Cheung Kathryn L.Stone Nicholas J.Carriero Erol E.Gulcicek TuKiet T.Lam Terence Wu Robert D.Bjornson Can Bruce Angus C.Nairn Jesse Rinehart Perry L.Miller Kenneth R.Williams 《基因组蛋白质组与生物信息学报(英文版)》2015,13(1):25-35
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. 相似文献
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Stone KL Bjornson RD Blasko GG Bruce C Cofrancesco R Carriero NJ Colangelo CM Crawford JK Crawford JM daSilva NC Deluca JD Elliott JI Elliott MM Flory PJ Folta-Stogniew EJ Gulcicek E Kong Y Lam TT Lee JY Lin A LoPresti MB Mane SM McMurray WJ Tikhonova IR Westman S Williams NA Wu TL Hongyu Z Williams KR 《The Yale journal of biology and medicine》2007,80(4):195-211
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Adil Mardinoglu Hao Wu Elias Bjornson Cheng Zhang Antti Hakkarainen Sari M. Räsänen Sunjae Lee Rosellina M. Mancina Mattias Bergentall Kirsi H. Pietiläinen Sanni Söderlund Niina Matikainen Marcus Ståhlman Per-Olof Bergh Martin Adiels Brian D. Piening Marit Granér Nina Lundbom Jan Borén 《Cell metabolism》2018,27(3):559-571.e5
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Mallikarjun S Beelagi SR Santosh Kumar Uma Bharathi Indrabalan Sharanagouda S Patil Ashwini Prasad KP Suresh Shiva Prasad Kollur Veeresh Santhebennur Jayappa Siddappa B Kakkalameli Chandrashekar Srinivasa Prabhakarareddy Anapalli Venkataravana Chandan Shivamallu 《Bioinformation》2021,17(4):479
Crimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias. 相似文献
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Tiffany Wang Perry Evans Antonella Bacchiocchi Robert Bjornson Elaine Cheng Amy L. Stiegler Symon Gathiaka Orlando Acevedo Titus J. Boggon Michael Krauthammer Ruth Halaban Tian Xu 《Pigment cell & melanoma research》2014,27(2):253-262
BRAF inhibitors improve melanoma patient survival, but resistance invariably develops. Here we report the discovery of a novel BRAF mutation that confers resistance to PLX4032 employing whole‐exome sequencing of drug‐resistant BRAFV600K melanoma cells. We further describe a new screening approach, a genome‐wide piggyBac mutagenesis screen that revealed clinically relevant aberrations (N‐terminal BRAF truncations and CRAF overexpression). The novel BRAF mutation, a Leu505 to His substitution (BRAFL505H), is the first resistance‐conferring second‐site mutation identified in BRAF mutant cells. The mutation replaces a small nonpolar amino acid at the BRAF‐PLX4032 interface with a larger polar residue. Moreover, we show that BRAFL505H, found in human prostate cancer, is itself a MAPK‐activating, PLX4032‐resistant oncogenic mutation. Lastly, we demonstrate that the PLX4032‐resistant melanoma cells are sensitive to novel, next‐generation BRAF inhibitors, especially the ‘paradox‐blocker’ PLX8394, supporting its use in clinical trials for treatment of melanoma patients with BRAF‐mutations. 相似文献
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Reactogenicity of trivalent influenza vaccine prepared for the 1988-89 season was assessed as part of a first-time voluntary influenza prevention program among hospital staff. Of approximately 500 full-time workers in areas with the highest concentrations of patients at high risk for influenza complications offered the vaccine 288 accepted. Of these, 266 (92%) returned a questionnaire regarding any symptoms experienced within 48 hours after vaccination; 238 (90%) of the respondents reported adverse effects. Soreness at the injection site was described by 229 subjects, 58 (25%) of whom had constant aching and 123 (54%) soreness with arm movement. Symptoms resolved in 1 to 2 days, and only 21 (9%) of those who reported symptoms said they took analgesic medication. Systemic adverse effects were described by 130 subjects (49%). Intercurrent illness accounted for some of these complaints, but 65 people (24%) described at least two of the following symptoms: generalized aching, tiredness, nausea, chills or onset of fever within 12 hours after vaccination (a symptom complex previously attributed to influenza vaccine). Systemic symptoms resolved within 0.5 to 2 days. Thirteen subjects (5%) reported missing work because of arm soreness (1 subject) or systemic symptoms (12). Adverse effects were encountered more often than expected, probably because most of the workers were young and lacked immunity to influenza. Acceptability of the program could likely be improved by using a split-virus vaccine. 相似文献
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