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Membrane-anchored substrate binding proteins are deployed in secondary TAXI transporters. 膜锚定的底物结合蛋白被部署在次级的士转运蛋白中。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-06-27 DOI: 10.1515/hsz-2022-0337
Anja Roden, Melanie K Engelin, Klaas M Pos, Eric R Geertsma
{"title":"Membrane-anchored substrate binding proteins are deployed in secondary TAXI transporters.","authors":"Anja Roden,&nbsp;Melanie K Engelin,&nbsp;Klaas M Pos,&nbsp;Eric R Geertsma","doi":"10.1515/hsz-2022-0337","DOIUrl":"https://doi.org/10.1515/hsz-2022-0337","url":null,"abstract":"<p><p>Substrate-binding proteins (SBPs) are part of solute transport systems and serve to increase substrate affinity and uptake rates. In contrast to primary transport systems, the mechanism of SBP-dependent secondary transport is not well understood. Functional studies have thus far focused on Na<sup>+</sup>-coupled Tripartite ATP-independent periplasmic (TRAP) transporters for sialic acid. Herein, we report the <i>in vitro</i> functional characterization of TAXIPm-PQM from the human pathogen <i>Proteus mirabilis</i>. TAXIPm-PQM belongs to a TRAP-subfamily using a different type of SBP, designated TRAP-associated extracytoplasmic immunogenic (TAXI) protein. TAXIPm-PQM catalyzes proton-dependent α-ketoglutarate symport and its SBP is an essential component of the transport mechanism. Importantly, TAXIPm-PQM represents the first functionally characterized SBP-dependent secondary transporter that does not rely on a soluble SBP, but uses a membrane-anchored SBP instead.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 7","pages":"715-725"},"PeriodicalIF":3.7,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9771990","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
Mycobacterial type VII secretion systems. 分枝杆菌VII型分泌系统。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-06-27 DOI: 10.1515/hsz-2022-0350
Nikolaos Famelis, Sebastian Geibel, Daan van Tol
{"title":"Mycobacterial type VII secretion systems.","authors":"Nikolaos Famelis,&nbsp;Sebastian Geibel,&nbsp;Daan van Tol","doi":"10.1515/hsz-2022-0350","DOIUrl":"https://doi.org/10.1515/hsz-2022-0350","url":null,"abstract":"<p><p>Mycobacteria, such as the pathogen <i>M. tuberculosis</i>, utilize up to five paralogous type VII secretion systems to transport proteins across their cell envelope. Since these proteins associate in pairs that depend on each other for transport to a different extent, the secretion pathway to the bacterial surface remained challenging to address. Structural characterization of the inner-membrane embedded secretion machineries along with recent advances on the substrates' co-dependencies for transport allow for the first time more detailed and testable models for secretion.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 7","pages":"691-702"},"PeriodicalIF":3.7,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9769080","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
ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy. 用时间分辨傅立叶变换红外光谱法监测全长MsbA中ATP结合和ATP水解。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-06-27 DOI: 10.1515/hsz-2023-0122
Daniel Mann, Kristin Labudda, Sophie Zimmermann, Kai Ulrich Vocke, Raphael Gasper, Carsten Kötting, Eckhard Hofmann
{"title":"ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy.","authors":"Daniel Mann,&nbsp;Kristin Labudda,&nbsp;Sophie Zimmermann,&nbsp;Kai Ulrich Vocke,&nbsp;Raphael Gasper,&nbsp;Carsten Kötting,&nbsp;Eckhard Hofmann","doi":"10.1515/hsz-2023-0122","DOIUrl":"https://doi.org/10.1515/hsz-2023-0122","url":null,"abstract":"<p><p>The essential <i>Escherichia coli</i> ATPase MsbA is a lipid flippase that serves as a prototype for multi drug resistant ABC transporters. Its physiological function is the transport of lipopolisaccharides to build up the outer membranes of Gram-negative bacteria. Although several structural and biochemical studies of MsbA have been conducted previously, a detailed picture of the dynamic processes that link ATP hydrolysis to allocrit transport remains elusive. We report here for the first time time-resolved Fourier transform infrared (FTIR) spectroscopic measurements of the ATP binding and ATP hydrolysis reaction of full-length MsbA and determined reaction rates at 288 K of <i>k</i> <sub>1</sub> = 0.49 ± 0.28 s<sup>-1</sup> and <i>k</i> <sub>2</sub> = 0.014 ± 0.003 s<sup>-1</sup>, respectively. We further verified these rates with photocaged NPE<i>cg</i>AppNHp where only nucleotide binding was observable and the negative mutant MsbA-H537A that showed slow hydrolysis (<i>k</i> <sub>2</sub> < 2 × 10<sup>-4</sup> s<sup>-1</sup>). Besides single turnover kinetics, FTIR measurements also deliver IR signatures of all educts, products and the protein. ADP remains protein-bound after ATP hydrolysis. In addition, the spectral changes observed for the two variants MsbA-S378A and MsbA-S482A correlated with the loss of hydrogen bonding to the γ-phosphate of ATP. This study paves the way for FTIR-spectroscopic investigations of allocrite transport in full-length MsbA.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 7","pages":"727-737"},"PeriodicalIF":3.7,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9759875","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
Interaction of RTX toxins with the host cell plasma membrane. RTX毒素与宿主细胞膜的相互作用。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-06-27 DOI: 10.1515/hsz-2022-0336
Feby M Chacko, Lutz Schmitt
{"title":"Interaction of RTX toxins with the host cell plasma membrane.","authors":"Feby M Chacko,&nbsp;Lutz Schmitt","doi":"10.1515/hsz-2022-0336","DOIUrl":"https://doi.org/10.1515/hsz-2022-0336","url":null,"abstract":"<p><p><b>R</b>epeats in <b>T</b>o<b>X</b>ins (RTX) protein family is a group of exoproteins secreted by Type 1 secretion system (T1SS) of several Gram-negative bacteria. The term RTX is derived from the characteristic nonapeptide sequence (GGxGxDxUx) present at the C-terminus of the protein. This RTX domain binds to calcium ions in the extracellular medium after being secreted out of the bacterial cells, and this facilitates folding of the entire protein. The secreted protein then binds to the host cell membrane and forms pores via a complex pathway, which eventually leads to the cell lysis. In this review, we summarize two different pathways in which RTX toxins interact with host cell membrane and discuss the possible reasons for specific and unspecific activity of RTX toxins to different types of host cells.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 7","pages":"663-671"},"PeriodicalIF":3.7,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10127902","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
Two are not enough: synthetic strategies and applications of unnatural base pairs. 两个还不够：合成策略和非自然碱基对的应用。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-06-26 Print Date: 2023-09-26 DOI: 10.1515/hsz-2023-0169
Robert Dörrenhaus, Philip K Wagner, Stephanie Kath-Schorr
{"title":"Two are not enough: synthetic strategies and applications of unnatural base pairs.","authors":"Robert Dörrenhaus,&nbsp;Philip K Wagner,&nbsp;Stephanie Kath-Schorr","doi":"10.1515/hsz-2023-0169","DOIUrl":"10.1515/hsz-2023-0169","url":null,"abstract":"<p><p>Nucleic acid chemistry is a rapidly evolving field, and the need for novel nucleotide modifications and artificial nucleotide building blocks for diagnostic and therapeutic use, material science or for studying cellular processes continues unabated. This review focusses on the development and application of unnatural base pairs as part of an expanded genetic alphabet. Not only recent developments in \"nature-like\" artificial base pairs are presented, but also current synthetic methods to get access to C-glycosidic nucleotides. Wide-ranging viability in synthesis is a prerequisite for the successful use of unnatural base pairs in a broader spectrum and will be discussed.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 10","pages":"883-896"},"PeriodicalIF":3.7,"publicationDate":"2023-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10272302","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 phase separation of the C-terminal domain of RNA polymerase II. RNA聚合酶C末端结构域的结构和相分离Ⅱ。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-06-20 Print Date: 2023-07-26 DOI: 10.1515/hsz-2023-0136
Irina P Lushpinskaia, David Flores-Solis, Markus Zweckstetter
{"title":"Structure and phase separation of the C-terminal domain of RNA polymerase II.","authors":"Irina P Lushpinskaia,&nbsp;David Flores-Solis,&nbsp;Markus Zweckstetter","doi":"10.1515/hsz-2023-0136","DOIUrl":"10.1515/hsz-2023-0136","url":null,"abstract":"<p><p>The repetitive heptads in the C-terminal domain (CTD) of RPB1, the largest subunit of RNA Polymerase II (Pol II), play a critical role in the regulation of Pol II-based transcription. Recent findings on the structure of the CTD in the pre-initiation complex determined by cryo-EM and the novel phase separation properties of key transcription components offers an expanded mechanistic interpretation of the spatiotemporal distribution of Pol II during transcription. Current experimental evidence further suggests an exquisite balance between CTD's local structure and an array of multivalent interactions that drive phase separation of Pol II and thus shape its transcriptional activity.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 8-9","pages":"839-844"},"PeriodicalIF":3.7,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10232883","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
Frontmatter 头版头条
4区 生物学
Biological Chemistry Pub Date : 2023-06-01 DOI: 10.1515/hsz-2023-frontmatter7
{"title":"Frontmatter","authors":"","doi":"10.1515/hsz-2023-frontmatter7","DOIUrl":"https://doi.org/10.1515/hsz-2023-frontmatter7","url":null,"abstract":"","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"28 23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136107829","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
Molecular simulations of DEAH-box helicases reveal control of domain flexibility by ligands: RNA, ATP, ADP, and G-patch proteins. DEAH-box解旋酶的分子模拟揭示了配体对结构域柔性的控制：RNA、ATP、ADP和G-补丁蛋白。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-05-31 Print Date: 2023-07-26 DOI: 10.1515/hsz-2023-0154
Robert A Becker, Jochen S Hub
{"title":"Molecular simulations of DEAH-box helicases reveal control of domain flexibility by ligands: RNA, ATP, ADP, and G-patch proteins.","authors":"Robert A Becker,&nbsp;Jochen S Hub","doi":"10.1515/hsz-2023-0154","DOIUrl":"10.1515/hsz-2023-0154","url":null,"abstract":"<p><p>DEAH-box helicases use the energy from ATP hydrolysis to translocate along RNA strands. They are composed of tandem RecA-like domains and a C-terminal domain connected by flexible linkers, and the activity of several DEAH-box helicases is regulated by cofactors called G-patch proteins. We used all-atom molecular dynamics simulations of the helicases Prp43, Prp22, and DHX15 in various liganded states to investigate how RNA, ADP, ATP, or G-patch proteins influence their conformational dynamics. The simulations suggest that apo helicases are highly flexible, whereas binding of RNA renders the helicases more rigid. ATP and ADP control the stability of the RecA1-RecA2 interface, but they have only a smaller effect on domain flexibility in absence of a RecA1-RecA2 interface. Binding of a G-patch protein to DHX15 imposes a more structured conformational ensemble, characterized by more defined relative domain arrangements and by an increased conformational stability of the RNA tunnel. However, the effect of the G-patch protein on domain dynamics is far more subtle as compared to the effects of RNA or ATP/ADP. The simulations characterize DEAH-box helicase as dynamic machines whose conformational ensembles are strongly defined by the presence of RNA, ATP, or ADP and only fine-tuned by the presence of G-patch proteins.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 8-9","pages":"867-879"},"PeriodicalIF":3.7,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10167391","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
Why do certain cancer cells alter functionality and fuse? 为什么某些癌症细胞会改变功能并融合？
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-05-30 Print Date: 2023-09-26 DOI: 10.1515/hsz-2023-0162
Thomas Dittmar, Mareike Sieler, Ralf Hass
{"title":"Why do certain cancer cells alter functionality and fuse?","authors":"Thomas Dittmar,&nbsp;Mareike Sieler,&nbsp;Ralf Hass","doi":"10.1515/hsz-2023-0162","DOIUrl":"10.1515/hsz-2023-0162","url":null,"abstract":"<p><p>Cancer cell fusion represents a rare event. However, the surviving cancer hybrid cells after a post-hybrid selection process (PHSP) can overgrow other cancer cells by exhibiting a proliferation advantage and/or expression of cancer stem-like properties. Addition of new tumor properties during hetero-fusion of cancer cells e.g. with mesenchymal stroma-/stem-like cells (MSC) contribute to enhanced tumor plasticity via acquisition of new/altered functionalities. This provides new avenues for tumor development and metastatic behavior. Consequently, the present review article will also address the question as to whether cancer cell fusion represents a general and possibly evolutionary-conserved program or rather a random process?</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":"404 10","pages":"951-960"},"PeriodicalIF":3.7,"publicationDate":"2023-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10627444","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
Illuminating the brain-genetically encoded single wavelength fluorescent biosensors to unravel neurotransmitter dynamics. 照亮大脑基因编码的单波长荧光生物传感器，揭示神经递质动力学。
IF 3.7 4区 生物学
Biological Chemistry Pub Date : 2023-05-30 Print Date: 2024-01-29 DOI: 10.1515/hsz-2023-0175
Martin Kubitschke, Olivia A Masseck
{"title":"Illuminating the brain-genetically encoded single wavelength fluorescent biosensors to unravel neurotransmitter dynamics.","authors":"Martin Kubitschke, Olivia A Masseck","doi":"10.1515/hsz-2023-0175","DOIUrl":"10.1515/hsz-2023-0175","url":null,"abstract":"<p><p>Understanding how neuronal networks generate complex behavior is one of the major goals of Neuroscience. Neurotransmitter and Neuromodulators are crucial for information flow between neurons and understanding their dynamics is the key to unravel their role in behavior. To understand how the brain transmits information and how brain states arise, it is essential to visualize the dynamics of neurotransmitters, neuromodulators and neurochemicals. In the last five years, an increasing number of single-wavelength biosensors either based on periplasmic binding proteins (PBPs) or on G-protein-coupled receptors (GPCR) have been published that are able to detect neurotransmitter release <i>in vitro</i> and <i>in vivo</i> with high spatial and temporal resolution. Here we review and discuss recent progress in the development of these sensors, their limitations and future directions.</p>","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":" ","pages":"55-65"},"PeriodicalIF":3.7,"publicationDate":"2023-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9586534","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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