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Erratum: Publisher Correction: Structural and chemical biology of deacetylases for carbohydrates, proteins, small molecules and histones.

ABSTRACT: [This corrects the article DOI: 10.1038/s42003-018-0214-4.].

SUBMITTER: Burger M

PROVIDER: S-EPMC6318210 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Structural and chemical biology of deacetylases for carbohydrates, proteins, small molecules and histones.

Project description:Deacetylation is the removal of an acetyl group and occurs on a plethora of targets and for a wide range of biological reasons. Several pathogens deacetylate their surface carbohydrates to evade immune response or to support biofilm formation. Furthermore, dynamic acetylation/deacetylation cycles govern processes from chromatin remodeling to posttranslational modifications that compete with phosphorylation. Acetylation usually occurs on nitrogen and oxygen atoms and are referred to as N- and O-acetylation, respectively. This review discusses the structural prerequisites that enzymes must have to catalyze the deacetylation reaction, and how they adapted by formation of specific substrate and metal binding sites.

| S-EPMC6281622 | biostudies-literature

Chemical and structural biology of protein lysine deacetylases.

Project description:Histone acetylation is a reversible posttranslational modification that plays a fundamental role in regulating eukaryotic gene expression and chromatin structure/function. Key enzymes for removing acetyl groups from histones are metal (zinc)-dependent and NAD+-dependent histone deacetylases (HDACs). The molecular function of HDACs have been extensively characterized by various approaches including chemical, molecular, and structural biology, which demonstrated that HDACs regulate cell proliferation, differentiation, and metabolic homeostasis, and that their alterations are deeply involved in various human disorders including cancer. Notably, drug discovery efforts have achieved success in developing HDAC-targeting therapeutics for treatment of several cancers. However, recent advancements in proteomics technology have revealed much broader aspects of HDACs beyond gene expression control. Not only histones but also a large number of cellular proteins are subject to acetylation by histone acetyltransferases (HATs) and deacetylation by HDACs. Furthermore, some of their structures can flexibly accept and hydrolyze other acyl groups on protein lysine residues. This review mainly focuses on structural aspects of HDAC enzymatic activity regulated by interaction with substrates, co-factors, small molecule inhibitors, and activators.

| S-EPMC5489435 | biostudies-literature

Erratum: Publisher Correction: Resource landscapes explain contrasting patterns of aggregation and site fidelity by red knots at two wintering sites.

Project description:[This corrects the article DOI: 10.1186/s40462-018-0142-4.].

| S-EPMC6385434 | biostudies-literature

Erratum: Correction of Acknowledgements.

Project description:[This corrects the article on p. 328 in vol. 61, PMID: 29780774.].

| S-EPMC6046364 | biostudies-literature

Designing Chimeric Molecules for Drug Discovery by Leveraging Chemical Biology.

Project description:After the first seed concept introduced in the 18th century, different disciplines have attributed different names to dual-functional molecules depending on their application, including bioconjugates, bifunctional compounds, multitargeting molecules, chimeras, hybrids, engineered compounds. However, these engineered constructs share a general structure: a first component that targets a specific cell and a second component that exerts the pharmacological activity. A stable or cleavable linker connects the two modules of a chimera. Herein, we discuss the recent advances in the rapidly expanding field of chimeric molecules leveraging chemical biology concepts. This Perspective is focused on bifunctional compounds in which one component is a lead compound or a drug. In detail, we discuss chemical features of chimeric molecules and their use for targeted delivery and for target engagement studies.

| S-EPMC7997565 | biostudies-literature

Publisher Correction: The role of Patronin in Drosophila mitosis.

Project description:During production of the original article [1], there was a technical error that resulted in author corrections not being rendered in the PDF version of the article.

| S-EPMC6615211 | biostudies-literature

Small molecules for cell reprogramming: a systems biology analysis.

Project description:If somatic stem cells would be able to maintain their regenerative capacity over time, this might, to a great extent, resolve rejuvenation issues. Unfortunately, the pool of somatic stem cells is limited, and they undergo cell aging with a consequent loss of functionality. During the last decade, low molecular weight compounds that are able to induce or enhance cell reprogramming have been reported. They were named "Small Molecules" (SMs) and might present definite advantages compared to the exogenous introduction of stemness-related transcription factors (e.g. Yamanaka's factors). Here, we undertook a systemic analysis of SMs and their potential gene targets. Data mining and curation lead to the identification of 92 SMs. The SM targets fall into three major functional categories: epigenetics, cell signaling, and metabolic "switchers". All these categories appear to be required in each SM cocktail to induce cell reprogramming. Remarkably, many enriched pathways of SM targets are related to aging, longevity, and age-related diseases, thus connecting them with cell reprogramming. The network analysis indicates that SM targets are highly interconnected and form protein-protein networks of a scale-free topology. The extremely high contribution of hubs to network connectivity suggests that (i) cell reprogramming may require SM targets to act cooperatively, and (ii) their network organization might ensure robustness by resistance to random failures. All in all, further investigation of SMs and their relationship with longevity regulators will be helpful for developing optimal SM cocktails for cell reprogramming with a perspective for rejuvenation and life span extension.

| S-EPMC8751603 | biostudies-literature

Publisher Correction: Understanding dynamic friction through spontaneously evolving laboratory earthquakes.

Project description:The HTML version of this Article incorrectly omits Supplementary Movie 1. Supplementary Movie 1 can be found as Supplementary Information associated with this Correction.

| S-EPMC6365550 | biostudies-literature

Publisher Correction to: TrancriptomeReconstructoR: data‑driven annotation of complex transcriptomes.

Project description: Not available

| S-EPMC8283902 | biostudies-literature

Chemical detoxification of small molecules by Caenorhabditis elegans.

Project description:Caenorhabditis elegans lives in compost and decaying fruit, eats bacteria and is exposed to pathogenic microbes. We show that C. elegans is able to modify diverse microbial small-molecule toxins via both O- and N-glucosylation as well as unusual 3'-O-phosphorylation of the resulting glucosides. The resulting glucosylated derivatives have significantly reduced toxicity to C. elegans, suggesting that these chemical modifications represent a general mechanism for worms to detoxify their environments.

| S-EPMC3747836 | biostudies-literature

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