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Colin M Hammond et al.
Molecular cell, 81(12), 2533-2548 (2021-04-16)
From biosynthesis to assembly into nucleosomes, histones are handed through a cascade of histone chaperones, which shield histones from non-specific interactions. Whether mechanisms exist to safeguard the histone fold during histone chaperone handover events or to release trapped intermediates is
Greta Caprara et al.
Journal of immunology (Baltimore, Md. : 1950), 200(7), 2439-2454 (2018-03-04)
The enzymes of the poly-ADP-ribose polymerase (PARP) superfamily control many relevant cellular processes, but a precise understanding of their activities in different physiological or disease contexts is largely incomplete. We found that transcription of several Parp genes was dynamically regulated
Yumiko Mizukoshi et al.
ChemMedChem, 10(4), 736-741 (2015-03-12)
Numerous small organic compounds exist in equilibrium among monomers, soluble oligomers, and insoluble aggregates in aqueous solution. Compound aggregation is a major reason for false positives in drug screening, and even soluble oligomers can interfere with structural and biochemical analyses.
Maria Emilia Taskinen et al.
The Journal of cell biology, 219(6) (2020-04-21)
Microtubule-associated serine/threonine-protein kinase-like (MASTL) is a mitosis-accelerating kinase with emerging roles in cancer progression. However, possible cell cycle-independent mechanisms behind its oncogenicity remain ambiguous. Here, we identify MASTL as an activator of cell contractility and MRTF-A/SRF (myocardin-related transcription factor A/serum
Yahui Yan et al.
Nature communications, 10(1), 541-541 (2019-02-03)
Despite its known role as a secreted neuroprotectant, much of the mesencephalic astrocyte-derived neurotrophic factor (MANF) is retained in the endoplasmic reticulum (ER) of producer cells. There, by unknown mechanisms, MANF plays a role in protein folding homeostasis in complex
Raghu R Edupuganti et al.
Nature structural & molecular biology, 24(10), 870-878 (2017-09-05)
RNA modifications are integral to the regulation of RNA metabolism. One abundant mRNA modification is N6-methyladenosine (m6A), which affects various aspects of RNA metabolism, including splicing, translation and degradation. Current knowledge about the proteins recruited to m6A to carry out
Patrycja Kozik et al.
Cell reports, 32(2), 107905-107905 (2020-07-16)
Cross-presentation of antigens by dendritic cells (DCs) is critical for initiation of anti-tumor immune responses. Yet, key steps involved in trafficking of antigens taken up by DCs remain incompletely understood. Here, we screen 700 US Food and Drug Administration (FDA)-approved drugs
Constance Alabert et al.
Cell reports, 30(4), 1223-1234 (2020-01-30)
Chromatin states must be maintained during cell proliferation to uphold cellular identity and genome integrity. Inheritance of histone modifications is central in this process. However, the histone modification landscape is challenged by incorporation of new unmodified histones during each cell
X Zheng et al.
Journal of dental research, 94(2), 344-353 (2014-12-06)
Dental caries is closely associated with the microbial disequilibrium between acidogenic/aciduric pathogens and alkali-generating commensal residents within the dental plaque. Fluoride is a widely used anticaries agent, which promotes tooth hard-tissue remineralization and suppresses bacterial activities. Recent clinical trials have
David Tobys et al.
Traffic (Copenhagen, Denmark), 22(1-2), 6-22 (2020-11-24)
In eukaryotic cells, clathrin-mediated endocytosis (CME) is a central pathway for the internalization of proteins from the cell surface, thereby contributing to the maintenance of the plasma membrane protein composition. A key component for the formation of endocytic clathrin-coated vesicles
Charlotte B Christiansen et al.
Physiological reports, 6(13), e13788-e13788 (2018-07-08)
Interleukin 6 (IL-6) is a cytokine secreted from skeletal muscle in response to exercise which, based on animal and cell studies, has been suggested to contribute to glucose metabolism by increasing secretion of the incretin hormone glucagon-like peptide-1 (GLP-1) and
Xiaofei Zhang et al.
Molecular cell, 65(5), 941-955 (2017-02-14)
Intracellular signaling via the covalent attachment of different ubiquitin linkages to protein substrates is fundamental to many cellular processes. Although linkage-selective ubiquitin interactors have been studied on a case-by-case basis, proteome-wide analyses have not been conducted yet. Here, we present
Nicholas Johnson et al.
Scientific reports, 7(1), 7283-7283 (2017-08-06)
Rhomboids are intramembrane serine proteases conserved in all kingdoms of life. They regulate epidermal growth factor receptor signalling in Drosophila by releasing signalling ligands from their transmembrane tethers. Their functions in mammals are poorly understood, in part because of the
Jenna Gallie et al.
PLoS biology, 13(3), e1002109-e1002109 (2015-03-13)
Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to
Chengjie Chen et al.
STAR protocols, 1(3), 100109-100109 (2020-12-31)
Protein-protein interactions (PPIs) play essential roles in almost all aspects of cellular processes. However, PPIs remain challenging to study due to their substoichiometry, low affinity, dynamic nature, and context dependence. Here, we present a protocol for the capture and identification
Sheng-Chieh Hsu et al.
Theranostics, 11(15), 7527-7545 (2021-06-24)
Rationale: One of the most common metabolic defects in cancers is the deficiency in arginine synthesis, which has been exploited therapeutically. Yet, challenges remain, and the mechanisms of arginine-starvation induced killing are largely unclear. Here, we sought to demonstrate the
Monica Soldi et al.
Molecular & cellular proteomics : MCP, 12(3), 764-780 (2013-01-16)
Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation.
Shota Someya et al.
iScience, 24(2), 102090-102090 (2021-02-23)
Human pluripotent stem cells (hPSCs) have a unique metabolic signature for maintenance of pluripotency, self-renewal, and survival. Although hPSCs could be potentially used in regenerative medicine, the prohibitive cost associated with large-scale cell culture presents a major barrier to the
Jenna K Rimel et al.
Genes & development, 34(21-22), 1452-1473 (2020-10-17)
CDK7 associates with the 10-subunit TFIIH complex and regulates transcription by phosphorylating the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Few additional CDK7 substrates are known. Here, using the covalent inhibitor SY-351 and quantitative phosphoproteomics, we identified CDK7 kinase
Tzu-Yu Liu et al.
Cell systems, 4(6), 636-644 (2017-06-06)
Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We
Daniel N Itzhak et al.
eLife, 5 (2016-06-10)
Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to
Katie Nightingale et al.
Cell host & microbe, 24(3), 447-460 (2018-08-21)
Human cytomegalovirus (HCMV) is an important pathogen with multiple immune evasion strategies, including virally facilitated degradation of host antiviral restriction factors. Here, we describe a multiplexed approach to discover proteins with innate immune function on the basis of active degradation
Alissa D Guarnaccia et al.
Cell reports, 34(3), 108636-108636 (2021-01-21)
The chromatin-associated protein WDR5 is a promising pharmacological target in cancer, with most drug discovery efforts directed against an arginine-binding cavity in WDR5 called the WIN site. Despite a clear expectation that WIN site inhibitors will alter the repertoire of
John M E Nichols et al.
Developmental cell, 48(4), 491-505 (2019-01-08)
Signaling from chemoattractant receptors activates the cytoskeleton of crawling cells for chemotaxis. We show using phosphoproteomics that different chemoattractants cause phosphorylation of the same core set of around 80 proteins in Dictyostelium cells. Strikingly, the majority of these are phosphorylated
Chloe R McDonald et al.
Science translational medicine, 10(431) (2018-03-09)
Reducing adverse birth outcomes due to malaria in pregnancy (MIP) is a global health priority. However, there are few safe and effective interventions. l-Arginine is an essential amino acid in pregnancy and an immediate precursor in the biosynthesis of nitric
David Goodwin et al.
Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals, 19(6), 517-529 (2014-07-26)
Mild injury of the exocrine pancreas is often asymptomatic and can be under- or mis-diagnosed. The pancreas-enriched microRNAs miR-216a and miR-217 were evaluated as potential serum biomarkers of exocrine pancreas injury in rodent models of acute pancreatitis induced by caerulein
Zhong-Qiu Yu et al.
Autophagy, 16(11), 2036-2051 (2020-01-17)
Macroautophagy (autophagy) is driven by the coordinated actions of core autophagy-related (Atg) proteins. Atg8, the core Atg protein generally considered acting most downstream, has recently been shown to interact with other core Atg proteins via their Atg8-family-interacting motifs (AIMs). However
Anne Ørgaard et al.
Islets, 11(5), 103-111 (2019-08-31)
The intestinal microbiota has been demonstrated to influence host metabolism, and has been proposed to affect the development of obesity and type 2 diabetes (T2D), possibly through short-chain fatty acids (SCFAs) produced by fermentation of dietary fiber. There are some
Sebastian Markmiller et al.
Cell, 172(3), 590-604 (2018-01-27)
Stress granules (SGs) are transient ribonucleoprotein (RNP) aggregates that form during cellular stress and are increasingly implicated in human neurodegeneration. To study the proteome and compositional diversity of SGs in different cell types and in the context of neurodegeneration-linked mutations
Rahul D Sheth et al.
Biotechnology and bioengineering, 111(8), 1595-1603 (2014-03-07)
In this work, a proof of concept elastin-like polypeptide-Z domain fusion (ELP-Z) based affinity precipitation process is developed for monoclonal antibody (mAb) purification from industrial harvest feeds. Greater than 99% mAb recoveries are obtained during the initial binding step of
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