Biological Chemistry最新文献_第2页

Analysis of cell cycle stage, replicated DNA, and chromatin-associated proteins using high-throughput flow cytometry. 利用高通量流式细胞仪分析细胞周期阶段、复制的 DNA 和染色质相关蛋白。

IF 2.9 4区生物学

Biological Chemistry Pub Date : 2024-09-03 DOI: 10.1515/hsz-2024-0058

Marina Bejarano Franco, Safia Boujataoui, Majd Hadji, Louis Hammer, Helle D Ulrich, L Maximilian Reuter

{"title":"Analysis of cell cycle stage, replicated DNA, and chromatin-associated proteins using high-throughput flow cytometry.","authors":"Marina Bejarano Franco, Safia Boujataoui, Majd Hadji, Louis Hammer, Helle D Ulrich, L Maximilian Reuter","doi":"10.1515/hsz-2024-0058","DOIUrl":"https://doi.org/10.1515/hsz-2024-0058","url":null,"abstract":"Flow cytometry is a versatile tool used for cell sorting, DNA content imaging, and determining various cellular characteristics. With the possibility of high-throughput analyses, it combines convenient labelling techniques to serve rapid, quantitative, and qualitative workflows. The ease of sample preparation and the broad range of applications render flow cytometry a preferred approach for many scientific questions. Yet, we lack practical adaptations to fully harness the quantitative and high-throughput capabilities of most cytometers for many organisms. Here, we present simple and advanced protocols for the analysis of total DNA content, de novo DNA synthesis, and protein association to chromatin in budding yeast and human cells. Upon optimization of experimental conditions and choice of fluorescent dyes, up to four parameters can be measured simultaneously and quantitatively for each cell of a population in a multi-well plate format. Reducing sample numbers, plastic waste, costs per well, and hands-on time without compromising signal quality or single-cell accuracy are the main advantages of the presented protocols. In proof-of-principle experiments, we show that DNA content increase in S-phase correlates with de novo DNA synthesis and can be predicted by the presence of the replicative helicase MCM2-7 on genomic DNA.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142143020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The TOM complex from an evolutionary perspective and the functions of TOMM70. 从进化角度看TOM复合体和TOMM70的功能。

IF 2.9 4区生物学

Biological Chemistry Pub Date : 2024-08-02 DOI: 10.1515/hsz-2024-0043

Metin Özdemir, Sven Dennerlein

引用次数: 0

Pathological and physiological roles of ADP-ribosylation: established functions and new insights ADP-ribosylation 的病理和生理作用：既有功能和新见解

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2024-07-26 DOI: 10.1515/hsz-2024-0057

Karla L.H. Feijs-Žaja, Nonso J. Ikenga, Roko Žaja

引用次数: 0

Insights in caveolae protein structure arrangements and their local lipid environment. 洞穴蛋白结构排列及其局部脂质环境的见解。

IF 2.9 4区生物学

Biological Chemistry Pub Date : 2024-07-08 DOI: 10.1515/hsz-2024-0046

Esther Ocket, Claudia Matthaeus

{"title":"Insights in caveolae protein structure arrangements and their local lipid environment.","authors":"Esther Ocket, Claudia Matthaeus","doi":"10.1515/hsz-2024-0046","DOIUrl":"https://doi.org/10.1515/hsz-2024-0046","url":null,"abstract":"Caveolae are 50-80 nm sized plasma membrane invaginations found in adipocytes, endothelial cells or fibroblasts. They are involved in endocytosis, lipid uptake and the regulation of the cellular lipid metabolism as well as sensing and adapting to changes in plasma membrane tension. Caveolae are characterized by their unique lipid composition and their specific protein coat consisting of caveolin and cavin proteins. Recently, detailed structural information was obtained for the major caveolae protein caveolin1 showing the formation of a disc-like 11-mer protein complex. Furthermore, the importance of the cavin disordered regions in the generation of cavin trimers and caveolae at the plasma membrane were revealed. Thus, finally, structural insights about the assembly of the caveolar coat can be elucidated. Here, we review recent developments in caveolae structural biology with regard to caveolae coat formation and caveolae curvature generation. Secondly, we discuss the importance of specific lipid species necessary for caveolae curvature and formation. In the last years, it was shown that specifically sphingolipids, cholesterol and fatty acids can accumulate in caveolae invaginations and may drive caveolae endocytosis. Throughout, we summarize recent studies in the field and highlight future research directions.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure, function, and recombinant production of EGFL7. EGFL7 的结构、功能和重组生产。

IF 2.9 4区生物学

Biological Chemistry Pub Date : 2024-05-29 DOI: 10.1515/hsz-2023-0358

Brennan McDonald, Mirko H H Schmidt

{"title":"Structure, function, and recombinant production of EGFL7.","authors":"Brennan McDonald, Mirko H H Schmidt","doi":"10.1515/hsz-2023-0358","DOIUrl":"10.1515/hsz-2023-0358","url":null,"abstract":"The secreted factor Epidermal growth factor-like protein 7 (EGFL7) is involved in angiogenesis, vasculogenesis, as well as neurogenesis. Importantly, EGFL7 is also implicated in various pathological conditions, including tumor angiogenesis in human cancers. Thus, understanding the mechanisms through which EGFL7 regulates and promotes blood vessel formation is of clear practical importance. One principle means by which EGFL7's function is investigated is via the expression and purification of the recombinant protein. This mini-review describes three methods used to produce recombinant EGFL7 protein. First, a brief overview of EGFL7's genetics, structure, and function is provided. This is followed by an examination of the advantages and disadvantages of three common expression systems used in the production of recombinant EGFL7; (i) Escherichia coli (E. coli), (ii) human embryonic kidney (HEK) 293 cells or other mammalian cells, and (iii) a baculovirus-based Sf9 insect cell expression system. Based on the available evidence, we conclude that the baculovirus-based Sf9 insect cell expression currently has the advantages of producing active recombinant EGFL7 in the native conformation with the presence of acceptable posttranslational modifications, while providing sufficient yield and stability for experimental purposes.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Beyond CAR T cells: exploring alternative cell sources for CAR-like cellular therapies. 超越 CAR T 细胞：探索 CAR 类细胞疗法的替代细胞来源。

IF 2.9 4区生物学

Biological Chemistry Pub Date : 2024-05-21 Print Date: 2024-07-26 DOI: 10.1515/hsz-2023-0317

Christina Angeliki Tsiverioti, Adrian Gottschlich, Marcel Trefny, Sebastian Theurich, Hans-Joachim Anders, Matthias Kroiss, Sebastian Kobold

引用次数: 0

Insights into caudate amphibian skin secretions with a focus on the chemistry and bioactivity of derived peptides. 洞察尾状两栖动物皮肤分泌物，重点关注衍生肽的化学性质和生物活性。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2024-05-21 DOI: 10.1515/hsz-2024-0035

Lorena Kröner, Stefan Lötters, Marie-T Hopp

{"title":"Insights into caudate amphibian skin secretions with a focus on the chemistry and bioactivity of derived peptides.","authors":"Lorena Kröner, Stefan Lötters, Marie-T Hopp","doi":"10.1515/hsz-2024-0035","DOIUrl":"https://doi.org/10.1515/hsz-2024-0035","url":null,"abstract":"Amphibians are well-known for their ability to produce and secrete a mixture of bioactive substances in specialized skin glands for the purpose of antibiotic self-protection and defense against predators. Some of these secretions contain various small molecules, such as the highly toxic batrachotoxin, tetrodotoxin, and samandarine. For some time, the presence of peptides in amphibian skin secretions has attracted researchers, consisting of a diverse collection of - to the current state of knowledge - three to 104 amino acid long sequences. From these more than 2000 peptides many are known to exert antimicrobial effects. In addition, there are some reports on amphibian skin peptides that can promote wound healing, regulate immunoreactions, and may serve as antiparasitic and antioxidative substances. So far, the focus has mainly been on skin peptides from frogs and toads (Anura), eclipsing the research on skin peptides of the ca. 700 salamanders and newts (Caudata). Just recently, several novel observations dealing with caudate peptides and their structure-function relationships were reported. This review focuses on the chemistry and bioactivity of caudate amphibian skin peptides and their potential as novel agents for clinical applications.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The complex regulation of Slo1 potassium channels from a structural perspective 从结构角度看 Slo1 钾通道的复杂调控

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2024-05-02 DOI: 10.1515/hsz-2024-0037

Tobias Raisch

{"title":"The complex regulation of Slo1 potassium channels from a structural perspective","authors":"Tobias Raisch","doi":"10.1515/hsz-2024-0037","DOIUrl":"https://doi.org/10.1515/hsz-2024-0037","url":null,"abstract":"Fast and regulated potassium efflux by Slo1 channels is crucial in many tissues in animals including neurons, the kidney and smooth muscle. During the last decade, structures have revealed many details about the gating mechanism and regulation of these large and complex molecular machines. This review summarizes these findings and the current knowledge about the intricate regulation of these important channels. Slo1 integrates sensing of the membrane potential via a voltage-sensor domain that undergoes subtle but significant structural rearrangements with a calcium-induced expansion of parts of the intracellular gating ring. Together, these two signals synergistically lead to changes in the conformation and chemical nature of the pore domain, allowing potassium ions to be translocated. In many native tissues, Slo1 channels are assembled with at least three classes of auxiliary subunits that change the gating kinetics or allow the channel to open also in absence of one of the two signals. Finally, Slo1 is inhibited, activated or deregulated by natural toxins and synthetic compounds, underlining the importance of the channel for the organism and as a potential target for drugs and other molecules.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"29 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140836897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unpaired cysteine insertions favor transmembrane dimerization and induce ligand-independent constitutive cytokine receptor signaling 非配对半胱氨酸插入有利于跨膜二聚化并诱导配体依赖性组成型细胞因子受体信号转导

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2024-05-02 DOI: 10.1515/hsz-2023-0344

Lynn Affrica Felicitas Baumgärtner, Julia Ettich, Helene Balles, Dorothee Johanna Lapp, Sofie Mossner, Christin Bassenge, Meryem Ouzin, Helmut Hanenberg, Jürgen Scheller, Doreen Manuela Floss

{"title":"Unpaired cysteine insertions favor transmembrane dimerization and induce ligand-independent constitutive cytokine receptor signaling","authors":"Lynn Affrica Felicitas Baumgärtner, Julia Ettich, Helene Balles, Dorothee Johanna Lapp, Sofie Mossner, Christin Bassenge, Meryem Ouzin, Helmut Hanenberg, Jürgen Scheller, Doreen Manuela Floss","doi":"10.1515/hsz-2023-0344","DOIUrl":"https://doi.org/10.1515/hsz-2023-0344","url":null,"abstract":"Naturally occurring gain-of-function (GOF) mutants have been identified in patients for a variety of cytokine receptors. Although this constitutive activation of cytokine receptors is strongly associated with malignant disorders, ligand-independent receptor activation is also a useful tool in synthetic biology e.g. to improve adoptive cellular therapies with genetically modified T-cells. Balanced Interleukin (IL-)7 signaling via a heterodimer of IL-7 receptor (IL-7Rα) and the common γ-chain (γc) controls T- and B-cell development and expansion, whereas uncontrolled IL-7 signaling can drive acute lymphoid leukemia (ALL) development. The ALL-driver mutation PPCL in the transmembrane domain of IL-7Rα is a mutational insertion of the four amino acids proline-proline-cysteine-leucine and leads to ligand-independent receptor dimerization and constitutive activation. We showed here in the cytokine-dependent pre-B-cell line Ba/F3 that the PPCL-insertion in a synthetic version of the IL-7Rα induced γc-independent STAT5 and ERK phosphorylation and also proliferation of the cells and that booster-stimulation by arteficial ligands additionally generated non-canonical STAT3 phosphorylation via the synthetic IL-7Rα-PPCL-receptors. Transfer of the IL-7Rα transmembrane domain with the PPCL insertion into natural and synthetic cytokine receptor chains of the IL-6, IL-12 and Interferon families also resulted in constitutive receptor signaling. In conclusion, our data suggested that the insertion of the mutated PPCL IL-7Rα transmembrane domain is an universal approach to generate ligand-independent, constitutively active cytokine receptors.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"3 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140836894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances in preclinical TCR characterization: leveraging cell avidity to identify functional TCRs 临床前 TCR 特征描述的进展：利用细胞亲和力识别功能性 TCR

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2024-04-26 DOI: 10.1515/hsz-2023-0341

Andreas Carr, Laura M. Mateyka, Sebastian J. C. Scheu, Ana Bici, Joris Paijmans, Rogier M. Reijmers, Nina Dieminger, Shirin Dildebekova, Noomen Hamed, Karolin Wagner, Dirk H. Busch, Elvira D’Ippolito

{"title":"Advances in preclinical TCR characterization: leveraging cell avidity to identify functional TCRs","authors":"Andreas Carr, Laura M. Mateyka, Sebastian J. C. Scheu, Ana Bici, Joris Paijmans, Rogier M. Reijmers, Nina Dieminger, Shirin Dildebekova, Noomen Hamed, Karolin Wagner, Dirk H. Busch, Elvira D’Ippolito","doi":"10.1515/hsz-2023-0341","DOIUrl":"https://doi.org/10.1515/hsz-2023-0341","url":null,"abstract":"T-cell therapy has emerged as an effective approach for treating viral infections and cancers. However, a significant challenge is the selection of T-cell receptors (TCRs) that exhibit the desired functionality. Conventionally in vitro techniques, such as peptide sensitivity measurements and cytotoxicity assays, provide valuable insights into TCR potency but are labor-intensive. In contrast, measuring ligand binding properties (z-Movi technology) could provide an accelerated processing while showing robust correlations with T-cell functions. In this study, we assessed whether cell avidity can predict functionality also in the context of TCR-engineered T cells. To this end, we developed a flexible system for TCR re-expression by generating a Jurkat-derived T cell clone lacking TCR and CD3 expression through CRISPR-Cas9-mediated TRBC knockout. The knockin of a transgenic TCR into the TRAC locus restored TCR/CD3 expression, allowing for CD3-based purification of TCR-engineered T cells. Subsequently, we characterized these engineered cell lines by functional readouts, and assessment of binding properties through the z-Movi technology. Our findings revealed a strong correlation between the cell avidities and functional sensitivities of Jurkat TCR-T cells. Altogether, by integrating cell avidity measurements with our versatile T cell engineering platform, we established an accelerated system for enhancing the in vitro selection of clinically relevant TCRs.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"49 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140798072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0