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Highlight: integrative structural biology of dynamic macromolecular assemblies. 推荐理由：动态大分子组装体的结构生物学一体化。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-08-08 Print Date: 2023-07-26 DOI: 10.1515/hsz-2023-0256
Ralf Ficner
{"title":"Highlight: integrative structural biology of dynamic macromolecular assemblies.","authors":"Ralf Ficner","doi":"10.1515/hsz-2023-0256","DOIUrl":"10.1515/hsz-2023-0256","url":null,"abstract":"","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 8-9","pages":"739"},"PeriodicalIF":3.7,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10177160","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
Crosstalk between cholesterol and PIP2 in the regulation of Kv7.2/Kv7.3 channels. 胆固醇和 PIP2 在调控 Kv7.2/Kv7.3 通道中的相互作用
IF 2.9 4区 生物学
Biological Chemistry Pub Date : 2023-08-08 Print Date: 2024-03-25 DOI: 10.1515/hsz-2023-0204
Mayra Delgado-Ramírez, Ana Laura López-Serrano, Sergio Sánchez-Armass, Ulises Meza, Aldo A Rodríguez-Menchaca
{"title":"Crosstalk between cholesterol and PIP<sub>2</sub> in the regulation of Kv7.2/Kv7.3 channels.","authors":"Mayra Delgado-Ramírez, Ana Laura López-Serrano, Sergio Sánchez-Armass, Ulises Meza, Aldo A Rodríguez-Menchaca","doi":"10.1515/hsz-2023-0204","DOIUrl":"10.1515/hsz-2023-0204","url":null,"abstract":"<p><p>The activity of neuronal Kv7.2/Kv7.3 channels is critically dependent on PIP<sub>2</sub> and finely modulated by cholesterol. Here, we report the crosstalk between cholesterol and PIP<sub>2</sub> in the regulation of Kv7.2/Kv7.3 channels. Our results show that currents passing through Kv7.2/Kv7.3 channels in cholesterol-depleted cells, by acute application of methyl-β-cyclodextrin (MβCD), were less sensitive to PIP<sub>2</sub> dephosphorylation strategies than those of control cells, suggesting that cholesterol depletion enhances the Kv7.2/Kv7.3-PIP<sub>2</sub> interaction. In contrast, the sensitivity of Kv7.2/Kv7.3 channels to acute membrane cholesterol depletion by MβCD was not altered in mutant channels with different apparent affinities for PIP<sub>2</sub>.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":"161-165"},"PeriodicalIF":2.9,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9962606","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 chromatin - triple helix connection. 染色质-三螺旋连接。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-07-31 Print Date: 2023-10-26 DOI: 10.1515/hsz-2023-0189
Rodrigo Maldonado, Gernot Längst
{"title":"The chromatin - triple helix connection.","authors":"Rodrigo Maldonado, Gernot Längst","doi":"10.1515/hsz-2023-0189","DOIUrl":"10.1515/hsz-2023-0189","url":null,"abstract":"<p><p>Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order genome organisation, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions. Different mechanisms allow the tethering of these chromatin-associated RNAs (caRNA) to chromosomes, including RNA binding proteins, the RNA polymerases and R-loops. In this review, we focus on the sequence-specific targeting of RNA to DNA by forming triple helical structures and describe its interplay with chromatin. It turns out that nucleosome positioning at triple helix target sites and the nucleosome itself are essential factors in determining the formation and stability of triple helices. The histone H3-tail plays a critical role in triple helix stabilisation, and the role of its epigenetic modifications in this process is discussed.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":"1037-1049"},"PeriodicalIF":3.7,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9885046","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
Bayesian methods in integrative structure modeling. 综合结构建模中的贝叶斯方法。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-07-31 Print Date: 2023-07-26 DOI: 10.1515/hsz-2023-0145
Michael Habeck
{"title":"Bayesian methods in integrative structure modeling.","authors":"Michael Habeck","doi":"10.1515/hsz-2023-0145","DOIUrl":"10.1515/hsz-2023-0145","url":null,"abstract":"<p><p>There is a growing interest in characterizing the structure and dynamics of large biomolecular assemblies and their interactions within the cellular environment. A diverse array of experimental techniques allows us to study biomolecular systems on a variety of length and time scales. These techniques range from imaging with light, X-rays or electrons, to spectroscopic methods, cross-linking mass spectrometry and functional genomics approaches, and are complemented by AI-assisted protein structure prediction methods. A challenge is to integrate all of these data into a model of the system and its functional dynamics. This review focuses on Bayesian approaches to integrative structure modeling. We sketch the principles of Bayesian inference, highlight recent applications to integrative modeling and conclude with a discussion of current challenges and future perspectives.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 8-9","pages":"741-754"},"PeriodicalIF":3.7,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10178504","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: 1
Structure and function of spliceosomal DEAH-box ATPases. 剪接体DEAH-box ATP酶的结构与功能。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-07-17 Print Date: 2023-07-26 DOI: 10.1515/hsz-2023-0157
Marieke Enders, Piotr Neumann, Achim Dickmanns, Ralf Ficner
{"title":"Structure and function of spliceosomal DEAH-box ATPases.","authors":"Marieke Enders,&nbsp;Piotr Neumann,&nbsp;Achim Dickmanns,&nbsp;Ralf Ficner","doi":"10.1515/hsz-2023-0157","DOIUrl":"10.1515/hsz-2023-0157","url":null,"abstract":"<p><p>Splicing of precursor mRNAs is a hallmark of eukaryotic cells, performed by a huge macromolecular machine, the spliceosome. Four DEAH-box ATPases are essential components of the spliceosome, which play an important role in the spliceosome activation, the splicing reaction, the release of the spliced mRNA and intron lariat, and the disassembly of the spliceosome. An integrative approach comprising X-ray crystallography, single particle cryo electron microscopy, single molecule FRET, and molecular dynamics simulations provided deep insights into the structure, dynamics and function of the spliceosomal DEAH-box ATPases.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 8-9","pages":"851-866"},"PeriodicalIF":3.7,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10179636","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
Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. 人类细胞中核糖体RNA前体的合成:机制、因素和调控。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-07-17 Print Date: 2023-10-26 DOI: 10.1515/hsz-2023-0214
Julia L Daiß, Joachim Griesenbeck, Herbert Tschochner, Christoph Engel
{"title":"Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation.","authors":"Julia L Daiß, Joachim Griesenbeck, Herbert Tschochner, Christoph Engel","doi":"10.1515/hsz-2023-0214","DOIUrl":"10.1515/hsz-2023-0214","url":null,"abstract":"Abstract The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":"1003-1023"},"PeriodicalIF":3.7,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10194199","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 DEAD-box RNA helicase Dbp5 is a key protein that couples multiple steps in gene expression. DEAD-box RNA解旋酶Dbp5是一种在基因表达中结合多个步骤的关键蛋白。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-07-13 Print Date: 2023-07-26 DOI: 10.1515/hsz-2023-0130
Luisa Querl, Heike Krebber
{"title":"The DEAD-box RNA helicase Dbp5 is a key protein that couples multiple steps in gene expression.","authors":"Luisa Querl,&nbsp;Heike Krebber","doi":"10.1515/hsz-2023-0130","DOIUrl":"10.1515/hsz-2023-0130","url":null,"abstract":"<p><p>Cell viability largely depends on the surveillance of mRNA export and translation. Upon pre-mRNA processing and nuclear quality control, mature mRNAs are exported into the cytoplasm via Mex67-Mtr2 attachment. At the cytoplasmic site of the nuclear pore complex, the export receptor is displaced by the action of the DEAD-box RNA helicase Dbp5. Subsequent quality control of the open reading frame requires translation. Our studies suggest an involvement of Dbp5 in cytoplasmic no-go-and non-stop decay. Most importantly, we have also identified a key function for Dbp5 in translation termination, which identifies this helicase as a master regulator of mRNA expression.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 8-9","pages":"845-850"},"PeriodicalIF":3.7,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10530721","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 human long non-coding RNA LINC00941 and its modes of action in health and disease. 人类长链非编码RNA LINC00941及其在健康和疾病中的作用模式。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-07-10 Print Date: 2023-10-26 DOI: 10.1515/hsz-2023-0183
Eva Morgenstern, Markus Kretz
{"title":"The human long non-coding RNA LINC00941 and its modes of action in health and disease.","authors":"Eva Morgenstern, Markus Kretz","doi":"10.1515/hsz-2023-0183","DOIUrl":"10.1515/hsz-2023-0183","url":null,"abstract":"<p><p>Long non-coding RNAs have gained attention in recent years as they were shown to play crucial roles in the regulation of cellular processes, but the understanding of the exact mechanisms is still incomplete in most cases. This is also true for long non-coding RNA LINC00941, which was recently found to be highly upregulated in various types of cancer influencing cell proliferation and metastasis. Initial studies could not elucidate the mode of action to understand the role and real impact of LINC00941 in tissue homeostasis and cancer development. However, recent analyses have demonstrated multiple potential modes of action of LINC00941 influencing the functionality of various cancer cell types. Correspondingly, LINC00941 was proposed to be involved in regulation of mRNA transcription and modulation of protein stability, respectively. In addition, several experimental approaches suggest a function of LINC00941 as competitive endogenous RNA, thus acting in a post-transcriptional regulatory fashion. This review summarizes our recent knowledge about the mechanisms of action of LINC00941 elucidated so far and discusses its putative role in miRNA sequestering processes. In addition, the functional role of LINC00941 in regulating human keratinocytes is discussed to also highlight its role in normal tissue homeostasis tissue aside from its involvement in cancer.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":"1025-1036"},"PeriodicalIF":3.7,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10212032","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: 2
Frontmatter 头版头条
4区 生物学
Biological Chemistry Pub Date : 2023-07-01 DOI: 10.1515/hsz-2023-frontmatter8-9
{"title":"Frontmatter","authors":"","doi":"10.1515/hsz-2023-frontmatter8-9","DOIUrl":"https://doi.org/10.1515/hsz-2023-frontmatter8-9","url":null,"abstract":"","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135804633","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
Translation termination in human mitochondria - substrate specificity of mitochondrial release factors. 人线粒体翻译终止——线粒体释放因子的底物特异性。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-06-29 Print Date: 2023-07-26 DOI: 10.1515/hsz-2023-0127
Franziska Nadler, Ricarda Richter-Dennerlein
{"title":"Translation termination in human mitochondria - substrate specificity of mitochondrial release factors.","authors":"Franziska Nadler,&nbsp;Ricarda Richter-Dennerlein","doi":"10.1515/hsz-2023-0127","DOIUrl":"10.1515/hsz-2023-0127","url":null,"abstract":"<p><p>Mitochondria are the essential players in eukaryotic ATP production by oxidative phosphorylation, which relies on the maintenance and accurate expression of the mitochondrial genome. Even though the basic principles of translation are conserved due to the descendance from a bacterial ancestor, some deviations regarding translation factors as well as mRNA characteristics and the applied genetic code are present in human mitochondria. Together, these features are certain challenges during translation the mitochondrion has to handle. Here, we discuss the current knowledge regarding mitochondrial translation focusing on the termination process and the associated quality control mechanisms. We describe how mtRF1a resembles bacterial RF1 mechanistically and summarize <i>in vitro</i> and recent <i>in vivo</i> data leading to the conclusion of mtRF1a being the major mitochondrial release factor. On the other hand, we discuss the ongoing debate about the function of the second codon-dependent mitochondrial release factor mtRF1 regarding its role as a specialized termination factor. Finally, we link defects in mitochondrial translation termination to the activation of mitochondrial rescue mechanisms highlighting the importance of ribosome-associated quality control for sufficient respiratory function and therefore for human health.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 8-9","pages":"769-779"},"PeriodicalIF":3.7,"publicationDate":"2023-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233378","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
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