Biological Chemistry最新文献

Simultaneous spectral illumination of microplates for high-throughput optogenetics and photobiology. 用于高通量光遗传学和光生物学的微孔板同步光谱照明。

IF 2.9 4区生物学

Biological Chemistry Pub Date : 2024-09-23 DOI: 10.1515/hsz-2023-0205

Arend Vogt, Raik Paulat, Daniel Parthier, Verena Just, Michal Szczepek, Patrick Scheerer, Qianzhao Xu, Andreas Möglich, Dietmar Schmitz, Benjamin R Rost, Nikolaus Wenger

{"title":"Simultaneous spectral illumination of microplates for high-throughput optogenetics and photobiology.","authors":"Arend Vogt, Raik Paulat, Daniel Parthier, Verena Just, Michal Szczepek, Patrick Scheerer, Qianzhao Xu, Andreas Möglich, Dietmar Schmitz, Benjamin R Rost, Nikolaus Wenger","doi":"10.1515/hsz-2023-0205","DOIUrl":"https://doi.org/10.1515/hsz-2023-0205","url":null,"abstract":"The biophysical characterization and engineering of optogenetic tools and photobiological systems has been hampered by the lack of efficient methods for spectral illumination of microplates for high-throughput analysis of action spectra. Current methods to determine action spectra only allow the sequential spectral illumination of individual wells. Here we present the open-source RainbowCap-system, which combines LEDs and optical filters in a standard 96-well microplate format for simultaneous and spectrally defined illumination. The RainbowCap provides equal photon flux for each wavelength, with the output of the LEDs narrowed by optical bandpass filters. We validated the RainbowCap for photoactivatable G protein-coupled receptors (opto-GPCRs) and enzymes for the control of intracellular downstream signaling. The simultaneous, spectrally defined illumination provides minimal interruption during time-series measurements, while resolving 10 nm differences in the action spectra of optogenetic proteins under identical experimental conditions. The RainbowCap is also suitable for studying the spectral dependence of light-regulated gene expression in bacteria, which requires illumination over several hours. In summary, the RainbowCap provides high-throughput spectral illumination of microplates, while its modular, customizable design allows easy adaptation to a wide range of optogenetic and photobiological applications.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280056","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

Protein persulfidation in plants: mechanisms and functions beyond a simple stress response. 植物中的蛋白质过硫化：超越简单应激反应的机制和功能。

IF 2.9 4区生物学

Biological Chemistry Pub Date : 2024-09-23 DOI: 10.1515/hsz-2024-0038

Anna Moseler, Stephan Wagner, Andreas J Meyer

{"title":"Protein persulfidation in plants: mechanisms and functions beyond a simple stress response.","authors":"Anna Moseler, Stephan Wagner, Andreas J Meyer","doi":"10.1515/hsz-2024-0038","DOIUrl":"https://doi.org/10.1515/hsz-2024-0038","url":null,"abstract":"Posttranslational modifications (PTMs) can modulate the activity, localization and interactions of proteins and (re)define their biological function. Understanding how changing environments can alter cellular processes thus requires detailed knowledge about the dynamics of PTMs in time and space. A PTM that gained increasing attention in the last decades is protein persulfidation, where a cysteine thiol (-SH) is covalently bound to sulfane sulfur to form a persulfide (-SSH). The precise cellular mechanisms underlying the presumed persulfide signaling in plants are, however, only beginning to emerge. In the mitochondrial matrix, strict regulation of persulfidation and H2S homeostasis is of prime importance for maintaining mitochondrial bioenergetic processes because H2S is a highly potent poison for cytochrome c oxidase. This review summarizes the current knowledge about protein persulfidation and corresponding processes in mitochondria of the model plant Arabidopsis. These processes will be compared to the respective processes in non-plant models to underpin similarities or highlight apparent differences. We provide an overview of mitochondrial pathways that contribute to H2S and protein persulfide generation and mechanisms for H2S fixation and de-persulfidation. Based on current proteomic data, we compile a plant mitochondrial persulfidome and discuss how persulfidation may regulate protein function.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280055","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 BCL11A transcription factor stimulates the enzymatic activities of the OGG1 DNA glycosylase BCL11A 转录因子刺激 OGG1 DNA 糖基化酶的酶活性

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2024-09-14 DOI: 10.1515/hsz-2024-0088

Tetiana Petrachkova, Olha Soldatkina, Lam Leduy, Alain Nepveu

{"title":"The BCL11A transcription factor stimulates the enzymatic activities of the OGG1 DNA glycosylase","authors":"Tetiana Petrachkova, Olha Soldatkina, Lam Leduy, Alain Nepveu","doi":"10.1515/hsz-2024-0088","DOIUrl":"https://doi.org/10.1515/hsz-2024-0088","url":null,"abstract":"The BCL11A transcription factor has previously been shown to interact with and stimulate the enzymatic activities of the NTHL1 DNA glycosylase and Pol β polymerase. Here we show that BCL11A and a smaller peptide encompassing amino acids 160 to 520 can interact with the 8-oxoguanine DNA glycosylase, OGG1, increase the binding of OGG1 to DNA that contains an 8-oxoguanine base and stimulate the glycosylase activity of OGG1. Following BCL11A knockdown, we observed an increase in oxidized purines in the genome using comet assays, while immunoassays reveal an increase in 8-oxoG bases. Structure-function analysis indicates that the stimulation of OGG1 by BCL11A requires the zinc fingers 1, 2 and 3 as well as the proline-rich region between the first and second zing finger, but a glutamate-rich region downstream of zinc finger 3 is dispensable. Ectopic expression of a small peptide that contains the three zinc fingers can rescue the increase in 8-oxoguanine caused by BCL11A knockdown. These findings, together with previous results showing that BCL11A stimulates the enzymatic activities of NTHL1 and the Pol β polymerase, suggest that high expression of BCL11A is important to protect cancer cells against oxidative DNA damage.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249468","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

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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