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141.
Marsilje TH Alper PB Lu W Mutnick D Michellys PY He Y Karanewsky DS Chow D Gerken A Lao J Kim MJ Seidel HM Tian SS 《Bioorganic & medicinal chemistry letters》2008,18(19):5259-5262
The lead optimization of a novel series of benzo[a]carbazole-based small molecule agonists of the thrombopoietin (Tpo) receptor is reported. The chemical instability of the dihydro-benzo[a]carbazole lead 2 was successfully addressed in the design and evaluation of compounds which also demonstrated improved potency compared to 2. Members of the scaffold have been identified which are full agonists that demonstrate cellular functional potency <50 nM. Analog 21 demonstrates equivalent efficacy in the human megakaryocyte differentiation (CFU-mega) assay compared to Eltrombopag. 相似文献
142.
The influence of peptide sequence and environment on the initiation and elongation of mucin O-glycosylation is not well understood. The in vivo glycosylation pattern of the porcine submaxillary gland mucin (PSM) tandem repeat containing 31 O-glycosylation sites (Gerken, T. A., Gilmore, M., and Zhang, J. (2002) J. Biol. Chem. 277, 7736-7751) reveals a weak inverse correlation with hydroxyamino acid density (and by inference the density of glycosylation) with the extent of GalNAc glycosylation and core-1 substitution. We now report the time course of the in vitro glycosylation of the apoPSM tandem repeat by recombinant UDP-GalNAc:polypeptide alpha-GalNAc transferases (ppGalNAc transferase) T1 and T2 that confirm these findings. A wide range of glycosylation rates are found, with several residues showing apparent plateaus in glycosylation. An adjustable kinetic model that reduces the first-order rate constants proportional to neighboring glycosylation status, plus or minus three residues of the site of glycosylation, was found to reasonably reproduce the experimental rate data for both transferases, including apparent plateaus in glycosylation. The unique, transferase-specific, positional weighting constants reveal information on the peptide/glycopeptide recognition site for each transferase. Both transferases displayed high sensitivities to neighboring Ser/Thr glycosylation, whereas ppGalNAc T2 displayed additional high sensitivities to the presence of nonglycosylated Ser/Thr residues. This is the first demonstration of the ability to model mucin O-glycosylation kinetics, confirming that under the appropriate conditions neighboring glycosylation status can be a significant factor modulating the first step of mucin O-glycan biosynthesis. 相似文献
143.
Multiple nuclear localization sequences allow modulation of 5-lipoxygenase nuclear import 总被引:1,自引:0,他引:1
The nuclear import of proteins typically requires the presence of a nuclear localization sequence (NLS). Some proteins have more than one NLS, but the significance of having multiple NLSs is unclear. The enzyme 5-lipoxygenase (5-LO) has three NLSs that, unlike the tight cluster of basic residues of the classical SV40 large T antigen NLS, contain dispersed basic residues. When attached to green fluorescent protein (GFP), individual 5-LO NLSs caused quantitatively and statistically less import than the SV40 NLS. Combined 5-LO NLSs produced nuclear import that was comparable to that of the SV40 NLS. As expected, GFP/NLS proteins displayed relatively uniform import in all cells. However, a fusion protein of GFP plus the 5-LO protein, modified to contain only one functional NLS, produced some cells with import and some cells without import. A GFP/5-LO fusion protein containing two functional NLSs produced four identifiable levels of nuclear import. Quantitative and visual analysis of a population of cells expressing the intact GFP/5-LO protein, with three intact NLSs, indicated five levels of nuclear import. This suggested that the subcellular distribution of 5-LO may vary widely in normal cells of the body. Consistent with this, immunohistochemical staining of lung sections found that individual macrophages, in situ, displayed cell-specific levels of import of 5-LO. Since nuclear accumulation is known to affect 5-LO activity, multiple NLSs may allow graded regulation of activity via controlled import. Multiple NLSs on other proteins may likewise allow fine control of protein action through modulation of the level of import. 相似文献
144.
Paul Roepman Erica de Koning Dik van Leenen Roel A de Weger J Alain Kummer Piet J Slootweg Frank CP Holstege 《Genome biology》2007,7(12):R117
Background
Metastasis, the process whereby cancer cells spread, is in part caused by an incompletely understood interplay between cancer cells and the surrounding stroma. Gene expression studies typically analyze samples containing tumor cells and stroma. Samples with less than 50% tumor cells are generally excluded, thereby reducing the number of patients that can benefit from clinically relevant signatures. 相似文献145.
Christian Kazenwadel Janosch Klebensberger Sven Richter Jens Pfannstiel Uwe Gerken Benjamin Pickel Andreas Schaller Bernhard Hauer 《Applied microbiology and biotechnology》2013,97(16):7215-7227
Phenoxy radical coupling reactions are involved in the biosynthesis of lignans in planta. Interestingly, the reaction can be guided by dirigent proteins, which mediate the stereoselective formation of either (+) or (?)-pinoresinol from coniferyl alcohol. So far, the mechanism is poorly understood, and for detailed mechanistic studies, a heterologous expression platform which allows the cost-effective, fast, and robust expression in high yields is needed. We established a reliable, high-yield fed-batch fermentation process with Pichia pastoris resulting in 47 mg?L?1 of the dirigent protein AtDIR6, which represents a more than 250-fold increase compared to previous studies. Biochemical characterization of AtDIR6 produced with P. pastoris showed an overall agreement in protein structure, N-glycosylation sites, and dirigent activity compared to AtDIR6 produced by plant cell cultures of Solanum peruvianum. CD spectroscopy verified the β-barrel structure proposed by earlier studies and bioconversion experiments revealed similar activities to plant-derived protein, validating P. pastoris as a suitable expression system for dirigent proteins. Compared to the complex glycan structures of most plant cells, proteins produced with P. pastoris have the advantage that they can be enzymatically deglycosylated under non-denaturating conditions. With this study, we demonstrate that the glycan structures of AtDIR6 are essential for structure, solubility, and function of the protein as deglycosylation induced conformational changes leading to the complete loss in dirigent activity and subsequent protein aggregation. 相似文献
146.
Zhihong Weng Judith Ertle Shaoping Zheng Thomas Lauenstein Stefan Mueller Andreas Bockisch Guido Gerken Dongliang Yang Joerg F. Schlaak 《PloS one》2013,8(12)
Aims
The current prognostic model to estimate the survival in hepatocellular carcinoma (HCC) patients treated with transarterial hepatic selective internal radiotherapy (SIRT) is not fully characterized. The aim of this study was to establish a new scoring model including assessment of both tumor responses and therapy-induced systemic changes in HCC patients to predict survival at an early time point post-SIRT.Methods and materials
Between 2008 and 2012, 149 HCC patients treated with SIRT were included into this study. CT images and biomarkers in blood tested at one month post-SIRT were analyzed and correlated with clinical outcome. Tumor responses were assessed by RECIST 1.1, mRECIST, and Choi criteria. Kaplan-Meier methods were used to estimate survival curves. Cox regression was used in uni- and multivariable survival analyses and in the establishment of a prognostic model.Results
A multivariate proportional hazards model was created based on the tumor response, the number of tumor nodules, the score of the model for end stage liver disease (MELD), and the serum C-reactive protein levels which were independent predictors of survival in HCC patients at one month post-SIRT. This prognostic model accurately differentiated the outcome of patients with different risk scores in this cohort (P<0.001). The model also had the ability to assign a predicted survival probability for individual patients.Conclusions
A new model to predict survival of HCC patients mainly based on tumor responses and therapy-induced systemic changes provides reliable prognosis and accurately discriminates the survival at an early time point after SIRT in these patients. 相似文献147.
Bas E Dutilh Cristiane C Thompson Ana CP Vicente Michel A Marin Clarence Lee Genivaldo GZ Silva Robert Schmieder Bruno GN Andrade Luciane Chimetto Daniel Cuevas Daniel R Garza Iruka N Okeke Aaron Oladipo Aboderin Jessica Spangler Tristen Ross Elizabeth A Dinsdale Fabiano L Thompson Timothy T Harkins Robert A Edwards 《BMC genomics》2014,15(1)
Background
Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.Results
Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.Conclusions
Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users. 相似文献148.
A replacement name is proposed for genus Dayus Gerken, 2001 (Crustacea: Peracarida: Cumacea), preoccupied by Dayus Mahmood, 1967 (Insecta: Hemiptera: Cicadellidae). The following changes are proposed: Jennidayus
new replacement name = Dayus Gerken, 2001 (nec Mahmood 1967); Jennidayus pharocheradus (Gerken, 2001), comb. n. = Dayus pharocheradus Gerken, 2001; Jennidayus acanthus (Gerken, 2001), comb. n. = Dayus acanthus Gerken, 2001; Jennidayus makrokolosus (Gerken, 2001), comb. n. = Dayus makrokolosus Gerken, 2001. 相似文献
149.
Joris J Benschop Tineke L Lenstra Dik van Leenen Marian JA Groot Koerkamp Thanasis Margaritis Mariel O Brok Patrick Kemmeren Frank CP Holstege 《Molecular systems biology》2014,10(6):732
Growth condition perturbation or gene function disruption are commonly used strategies to study cellular systems. Although it is widely appreciated that such experiments may involve indirect effects, these frequently remain uncharacterized. Here, analysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common gene expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response (ESR), an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response in single cells, both the slow growth signature and ESR mainly reflect a redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. 相似文献
150.
Aggrecan, a large chondroitin sulfate (CS) and keratan sulfate (KS) proteoglycan, has not previously been expressed as a full-length recombinant molecule. To facilitate structure/function analysis, we have characterized recombinant bovine aggrecan (rbAgg) and link protein expressed in COS-7 cells. We demonstrate that C-terminally truncated rbAgg was not secreted. Gel filtration chromatography of rbAgg and isolated glycosaminoglycan (GAG) chains, and their susceptibility to chondroitinase ABC digestion indicate that the GAG chains are predominantly CS, which likely occupy fewer serine residues than native aggrecan. To confirm functionality, we determined that rbAgg bound hyaluronan and recombinant link protein to form proteoglycan aggregates. In addition, cleavage of rbAgg by ADAMTS-4 revealed that the p68 form of ADAMTS-4 preferentially cleaves within the CS-2 domain, whereas the p40 form only effectively cleaves within the interglobular domain (IGD). MMP-13 cleaved rbAgg within the IGD, but cleaved more rapidly at a site within the CS domains, suggesting a role in C-terminal processing of aggrecan. Our results demonstrate that recombinant aggrecan can be used for in vitro analyses of matrix protease-dependent degradation of aggrecan in the IGD and CS domains, and both recombinant aggrecan and link protein can be used to study the assembly of proteoglycan aggregates with hyaluronan. 相似文献