Journal of Molecular Biology最新文献

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Regulated Proteolysis Induces Aberrant Phase Transition of Biomolecular Condensates into Aggregates: A Protective Role for the Chaperone Clusterin 调节蛋白水解诱导生物分子凝聚物向聚集体的异常相变;伴侣蛋白Clusterin的保护作用。
IF 4.7 2区 生物学
Journal of Molecular Biology Pub Date : 2024-10-28 DOI: 10.1016/j.jmb.2024.168839
Janine Kamps , Patricia Yuste-Checa , Fatemeh Mamashli , Matthias Schmitz , Maria Georgina Herrera , Susana Margarida da Silva Correia , Kalpshree Gogte , Verian Bader , Inga Zerr , F. Ulrich Hartl , Andreas Bracher , Konstanze F. Winklhofer , Jörg Tatzelt
{"title":"Regulated Proteolysis Induces Aberrant Phase Transition of Biomolecular Condensates into Aggregates: A Protective Role for the Chaperone Clusterin","authors":"Janine Kamps ,&nbsp;Patricia Yuste-Checa ,&nbsp;Fatemeh Mamashli ,&nbsp;Matthias Schmitz ,&nbsp;Maria Georgina Herrera ,&nbsp;Susana Margarida da Silva Correia ,&nbsp;Kalpshree Gogte ,&nbsp;Verian Bader ,&nbsp;Inga Zerr ,&nbsp;F. Ulrich Hartl ,&nbsp;Andreas Bracher ,&nbsp;Konstanze F. Winklhofer ,&nbsp;Jörg Tatzelt","doi":"10.1016/j.jmb.2024.168839","DOIUrl":"10.1016/j.jmb.2024.168839","url":null,"abstract":"<div><div>Several proteins associated with neurodegenerative diseases, such as the mammalian prion protein (PrP), undergo liquid–liquid phase separation (LLPS), which led to the hypothesis that condensates represent precursors in the formation of neurotoxic protein aggregates. However, the mechanisms that trigger aberrant phase separation are incompletely understood. In prion diseases, protease-resistant and infectious amyloid fibrils are composed of N-terminally truncated PrP, termed C2-PrP. C2-PrP is generated by regulated proteolysis (β-cleavage) of the cellular prion protein (PrP<sup>C</sup>) specifically upon prion infection, suggesting that C2-PrP is a misfolding-prone substrate for the propagation of prions. Here we developed a novel assay to investigate the role of both LLPS and β-cleavage in the formation of C2-PrP aggregates. We show that β-cleavage induces the formation of C2-PrP aggregates, but only when full-length PrP had formed biomolecular condensates via LLPS before proteolysis. In contrast, C2-PrP remains soluble after β-cleavage of non-phase-separated PrP. To investigate whether extracellular molecular chaperones modulate LLPS of PrP and/or misfolding of C2-PrP, we focused on Clusterin. Clusterin does not inhibit LLPS of full-length PrP, however, it prevents aggregation of C2-PrP after β-cleavage of phase-separated PrP. Furthermore, Clusterin interferes with the <em>in vitro</em> amplification of infectious human prions isolated from Creutzfeldt-Jakob disease patients. Our study revealed that regulated proteolysis triggers aberrant phase transition of biomolecular condensates into aggregates and identified Clusterin as a component of the extracellular quality control pathway to prevent the formation and propagation of pathogenic PrP conformers.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 23","pages":"Article 168839"},"PeriodicalIF":4.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cryo-EM Structures of the Plasmodium falciparum Apicoplast DNA Polymerase 恶性疟原虫 apicoplast DNA 聚合酶的冷冻电镜结构。
IF 4.7 2区 生物学
Journal of Molecular Biology Pub Date : 2024-10-26 DOI: 10.1016/j.jmb.2024.168842
Chen-Yu Lo , Adron R. Ung , Tirthankar Koley , Scott W. Nelson , Yang Gao
{"title":"Cryo-EM Structures of the Plasmodium falciparum Apicoplast DNA Polymerase","authors":"Chen-Yu Lo ,&nbsp;Adron R. Ung ,&nbsp;Tirthankar Koley ,&nbsp;Scott W. Nelson ,&nbsp;Yang Gao","doi":"10.1016/j.jmb.2024.168842","DOIUrl":"10.1016/j.jmb.2024.168842","url":null,"abstract":"<div><div>The apicoplast DNA polymerase (apPol) from Plasmodium falciparum is essential for the parasite’s survival, making it a prime target for antimalarial therapies. Here, we present cryo-electron microscopy structures of the apPol in complex with DNA and incoming nucleotide, offering insights into its molecular mechanisms. Our structural analysis reveals that apPol contains critical residues for high-fidelity DNA synthesis, but lacks certain structural elements to confer processive DNA synthesis during replication, suggesting the presence of additional accessory factors. The enzyme exhibits large-scale conformational changes upon DNA and nucleotide binding, particularly within the fingers and thumb subdomains. These movements reveal potential allosteric sites that could serve as targets for drug design. Our findings provide a foundation for advancing the understanding of apPol’s unique functional mechanisms and potentially offering new avenues for the development of novel inhibitors and therapeutic interventions against malaria.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 23","pages":"Article 168842"},"PeriodicalIF":4.7,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Identification of a Non-canonical Function of Prefoldin Subunit 5 in Proteasome Assembly 鉴定前折叠素亚基 5 在蛋白酶体组装中的非规范功能。
IF 4.7 2区 生物学
Journal of Molecular Biology Pub Date : 2024-10-26 DOI: 10.1016/j.jmb.2024.168838
Somayeh Shahmoradi Ghahe , Krzysztof Drabikowski , Monika Stasiak , Ulrike Topf
{"title":"Identification of a Non-canonical Function of Prefoldin Subunit 5 in Proteasome Assembly","authors":"Somayeh Shahmoradi Ghahe ,&nbsp;Krzysztof Drabikowski ,&nbsp;Monika Stasiak ,&nbsp;Ulrike Topf","doi":"10.1016/j.jmb.2024.168838","DOIUrl":"10.1016/j.jmb.2024.168838","url":null,"abstract":"<div><div>The prefoldin complex is a heterohexameric, evolutionarily conserved co-chaperone that assists in folding of polypeptides downstream of the protein translation machinery. Loss of prefoldin function leads to impaired solubility of cellular proteins. The degradation of proteins by the proteasome is an integral part of protein homeostasis. Failure of regulated protein degradation can lead to the accumulation of misfolded and defective proteins. We show that prefoldin subunit 5 is required for proteasome activity by contributing to the assembly of the 26S proteasome. In particular, we found that absence of the prefoldin subunit 5 impairs formation of the Rpt ring subcomplex of the proteasome. Concomitant deletion of <em>PFD5</em> and <em>HSM3</em>, a chaperone for assembly of the ATPase subunits comprising the Rpt ring, exacerbates this effect, suggesting a synergistic relationship between the two factors in proteasome assembly. Thus, our findings reveal a regulatory mechanism wherein prefoldin subunit 5 plays a crucial role in maintaining proteasome integrity, thereby influencing the degradation of proteins.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 23","pages":"Article 168838"},"PeriodicalIF":4.7,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 HSP90/R2TP Quaternary Chaperone Scaffolds Assembly of the TSC Complex HSP90/R2TP四级伴侣支架了TSC复合体的组装。
IF 4.7 2区 生物学
Journal of Molecular Biology Pub Date : 2024-10-26 DOI: 10.1016/j.jmb.2024.168840
Claire Abéza , Philipp Busse , Ana C.F. Paiva , Marie-Eve Chagot , Justine Schneider , Marie-Cécile Robert , Franck Vandermoere , Christine Schaeffer , Bruno Charpentier , Pedro M.F. Sousa , Tiago M. Bandeiras , Xavier Manival , Sarah Cianferani , Edouard Bertrand , Céline Verheggen
{"title":"The HSP90/R2TP Quaternary Chaperone Scaffolds Assembly of the TSC Complex","authors":"Claire Abéza ,&nbsp;Philipp Busse ,&nbsp;Ana C.F. Paiva ,&nbsp;Marie-Eve Chagot ,&nbsp;Justine Schneider ,&nbsp;Marie-Cécile Robert ,&nbsp;Franck Vandermoere ,&nbsp;Christine Schaeffer ,&nbsp;Bruno Charpentier ,&nbsp;Pedro M.F. Sousa ,&nbsp;Tiago M. Bandeiras ,&nbsp;Xavier Manival ,&nbsp;Sarah Cianferani ,&nbsp;Edouard Bertrand ,&nbsp;Céline Verheggen","doi":"10.1016/j.jmb.2024.168840","DOIUrl":"10.1016/j.jmb.2024.168840","url":null,"abstract":"<div><div>The R2TP chaperone is composed of the RUVBL1/RUVBL2 AAA+ ATPases and two adapter proteins, RPAP3 and PIH1D1. Together with HSP90, it functions in the assembly of macromolecular complexes that are often involved in cell proliferation. Here, proteomic experiments using the isolated PIH domain reveals additional R2TP partners, including the Tuberous Sclerosis Complex (TSC) and many transcriptional complexes. The TSC is a key regulator of mTORC1 and is composed of TSC1, TSC2 and TBC1D7. We show a direct interaction of TSC1 with the PIH phospho-binding domain of PIH1D1, which is, surprisingly, phosphorylation independent. Via the use of mutants and KO cell lines, we observe that TSC2 makes independent interactions with HSP90 and the TPR domains of RPAP3. Moreover, inactivation of PIH1D1 or the RUVBL1/2 ATPase activity inhibits the association of TSC1 with TSC2. Taken together, these data suggest a model in which the R2TP recruits TSC1 via PIH1D1 and TSC2 via RPAP3 and HSP90, and use the chaperone-like activities of RUVBL1/2 to stimulate their assembly.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 23","pages":"Article 168840"},"PeriodicalIF":4.7,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
GEMimp: An Accurate and Robust Imputation Method for Microbiome Data Using Graph Embedding Neural Network GEMimp:利用图嵌入神经网络对微生物组数据进行准确而稳健的估算方法。
IF 4.7 2区 生物学
Journal of Molecular Biology Pub Date : 2024-10-26 DOI: 10.1016/j.jmb.2024.168841
Ziwei Sun, Kai Song
{"title":"GEMimp: An Accurate and Robust Imputation Method for Microbiome Data Using Graph Embedding Neural Network","authors":"Ziwei Sun,&nbsp;Kai Song","doi":"10.1016/j.jmb.2024.168841","DOIUrl":"10.1016/j.jmb.2024.168841","url":null,"abstract":"<div><div>Microbiome research has increasingly underscored the profound link between microbial compositions and human health, with numerous studies establishing a strong correlation between microbiome characteristics and various diseases. However, the analysis of microbiome data is frequently compromised by inherent sparsity issues, characterized by a substantial presence of observed zeros. These zeros not only skew the abundance distribution of microbial species but also undermine the reliability of scientific conclusions drawn from such data. Addressing this challenge, we introduce GEMimp, an innovative imputation method designed to infuse robustness into microbiome data analysis. GEMimp leverages the node2vec algorithm, which incorporates both Breadth-First Search (BFS) and Depth-First Search (DFS) strategies in its random walks sampling process. This approach enables GEMimp to learn nuanced, low-dimensional representations of each taxonomic unit, facilitating the reconstruction of their similarity networks with unprecedented accuracy.</div><div>Our comparative analysis pits GEMimp against state-of-the-art imputation methods including SAVER, MAGIC and mbImpute. The results unequivocally demonstrate that GEMimp outperforms its counterparts by achieving the highest Pearson correlation coefficient when compared to the original raw dataset. Furthermore, GEMimp shows notable proficiency in identifying significant taxa, enhancing the detection of disease-related taxa and effectively mitigating the impact of sparsity on both simulated and real-world datasets, such as those pertaining to Type 2 Diabetes (T2D) and Colorectal Cancer (CRC). These findings collectively highlight the strong effectiveness of GEMimp, allowing for better analysis on microbial data. With alleviation of sparsity issues, it could be greatly facilitated in downstream analyses and even in the field of microbiology.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 23","pages":"Article 168841"},"PeriodicalIF":4.7,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Optogenetic Control of Condensates: Principles and Applications 冷凝物的光遗传学控制:原理与应用。
IF 4.7 2区 生物学
Journal of Molecular Biology Pub Date : 2024-10-24 DOI: 10.1016/j.jmb.2024.168835
Zikang Dennis Huang , Lukasz J. Bugaj
{"title":"Optogenetic Control of Condensates: Principles and Applications","authors":"Zikang Dennis Huang ,&nbsp;Lukasz J. Bugaj","doi":"10.1016/j.jmb.2024.168835","DOIUrl":"10.1016/j.jmb.2024.168835","url":null,"abstract":"<div><div>Biomolecular condensates appear throughout cell physiology and pathology, but the specific role of condensation or its dynamics is often difficult to determine. Optogenetics offers an expanding toolset to address these challenges, providing tools to directly control condensation of arbitrary proteins with precision over their formation, dissolution, and patterning in space and time. In this review, we describe the current state of the field for optogenetic control of condensation. We survey the proteins and their derivatives that form the foundation of this toolset, and we discuss the factors that distinguish them to enable appropriate selection for a given application. We also describe recent examples of the ways in which optogenetic condensation has been used in both basic and applied studies. Finally, we discuss important design considerations when engineering new proteins for optogenetic condensation, and we preview future innovations that will further empower this toolset in the coming years.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 23","pages":"Article 168835"},"PeriodicalIF":4.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Engineering Bacteriophytochrome-coupled Photoactivated Adenylyl Cyclases for Enhanced Optogenetic cAMP Modulation 设计细菌色素耦合光激活腺苷酸环化酶以增强光遗传学 cAMP 调节能力
IF 5.6 2区 生物学
Journal of Molecular Biology Pub Date : 2024-03-01 DOI: 10.1016/j.jmb.2023.168257
Qianzhao Xu , Arend Vogt , Fabian Frechen , Chengwei Yi , Melike Küçükerden , Neville Ngum , Laia Sitjà-Roqueta , Andreas Greiner , Rhein Parri , Mercè Masana , Nikolaus Wenger , Dagmar Wachten , Andreas Möglich
{"title":"Engineering Bacteriophytochrome-coupled Photoactivated Adenylyl Cyclases for Enhanced Optogenetic cAMP Modulation","authors":"Qianzhao Xu ,&nbsp;Arend Vogt ,&nbsp;Fabian Frechen ,&nbsp;Chengwei Yi ,&nbsp;Melike Küçükerden ,&nbsp;Neville Ngum ,&nbsp;Laia Sitjà-Roqueta ,&nbsp;Andreas Greiner ,&nbsp;Rhein Parri ,&nbsp;Mercè Masana ,&nbsp;Nikolaus Wenger ,&nbsp;Dagmar Wachten ,&nbsp;Andreas Möglich","doi":"10.1016/j.jmb.2023.168257","DOIUrl":"10.1016/j.jmb.2023.168257","url":null,"abstract":"<div><p>Sensory photoreceptors abound in nature and enable organisms to adapt behavior, development, and physiology to environmental light. In optogenetics, photoreceptors allow spatiotemporally precise, reversible, and non-invasive control by light of cellular processes. Notwithstanding the development of numerous optogenetic circuits, an unmet demand exists for efficient systems sensitive to red light, given its superior penetration of biological tissue. Bacteriophytochrome photoreceptors sense the ratio of red and far-red light to regulate the activity of enzymatic effector modules. The recombination of bacteriophytochrome photosensor modules with cyclase effectors underlies photoactivated adenylyl cyclases (PAC) that catalyze the synthesis of the ubiquitous second messenger 3′, 5′-cyclic adenosine monophosphate (cAMP). Via homologous exchanges of the photosensor unit, we devised novel PACs, with the variant <em>Dm</em>PAC exhibiting 40-fold activation of cyclase activity under red light, thus surpassing previous red-light-responsive PACs. Modifications of the PHY tongue modulated the responses to red and far-red light. Exchanges of the cyclase effector offer an avenue to further enhancing PACs but require optimization of the linker to the photosensor. <em>Dm</em>PAC and a derivative for 3′, 5′-cyclic guanosine monophosphate allow the manipulation of cyclic-nucleotide-dependent processes in mammalian cells by red light. Taken together, we advance the optogenetic control of second-messenger signaling and provide insight into the signaling and design of bacteriophytochrome receptors.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 5","pages":"Article 168257"},"PeriodicalIF":5.6,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283623003686/pdfft?md5=f69bd8b2b1c67f6fd9f1af3e6125635e&pid=1-s2.0-S0022283623003686-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10260078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response 通过从光吸收到构象反应的原子建模解密感光体。
IF 5.6 2区 生物学
Journal of Molecular Biology Pub Date : 2024-03-01 DOI: 10.1016/j.jmb.2023.168358
Giacomo Salvadori, Patrizia Mazzeo, Davide Accomasso, Lorenzo Cupellini, Benedetta Mennucci
{"title":"Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response","authors":"Giacomo Salvadori,&nbsp;Patrizia Mazzeo,&nbsp;Davide Accomasso,&nbsp;Lorenzo Cupellini,&nbsp;Benedetta Mennucci","doi":"10.1016/j.jmb.2023.168358","DOIUrl":"10.1016/j.jmb.2023.168358","url":null,"abstract":"<div><p>In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 5","pages":"Article 168358"},"PeriodicalIF":5.6,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283623004692/pdfft?md5=dc8527fa07c49af4bff89a40caf36310&pid=1-s2.0-S0022283623004692-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72012933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Channel Gating in Kalium Channelrhodopsin Slow Mutants 钾通道视紫红质慢突变体的通道门控。
IF 5.6 2区 生物学
Journal of Molecular Biology Pub Date : 2024-03-01 DOI: 10.1016/j.jmb.2023.168298
Oleg A. Sineshchekov, Elena G. Govorunova, Hai Li, Yumei Wang, John L. Spudich
{"title":"Channel Gating in Kalium Channelrhodopsin Slow Mutants","authors":"Oleg A. Sineshchekov,&nbsp;Elena G. Govorunova,&nbsp;Hai Li,&nbsp;Yumei Wang,&nbsp;John L. Spudich","doi":"10.1016/j.jmb.2023.168298","DOIUrl":"10.1016/j.jmb.2023.168298","url":null,"abstract":"<div><p>Kalium channelrhodopsin 1 from <em>Hyphochytrium catenoides</em> (<em>Hc</em>KCR1) is the first discovered natural light-gated ion channel that shows higher selectivity to K<sup>+</sup> than to Na<sup>+</sup> and therefore is used to silence neurons with light (optogenetics). Replacement of the conserved cysteine residue in the transmembrane helix 3 (Cys110) with alanine or threonine results in a &gt;1,000-fold decrease in the channel closing rate. The phenotype of the corresponding mutants in channelrhodopsin 2 is attributed to breaking of a specific interhelical hydrogen bond (the “DC gate”). Unlike <em>Cr</em>ChR2 and other ChRs with long distance “DC gates”, the <em>Hc</em>KCR1 structure does not reveal any hydrogen bonding partners to Cys110, indicating that the mutant phenotype is likely caused by disruption of direct interaction between this residue and the chromophore. In <em>Hc</em>KCR1_C110A, fast photochemical conversions corresponding to channel gating were followed by dramatically slower absorption changes. Full recovery of the unphotolyzed state in <em>Hc</em>KCR1_C110A was extremely slow with two time constants 5.2 and 70 min. Analysis of the light-minus-dark difference spectra during these slow processes revealed accumulation of at least four spectrally distinct blue light-absorbing photocycle intermediates, L, M<sub>1</sub> and M<sub>2</sub>, and a UV light-absorbing form, typical of bacteriorhodopsin-like channelrhodopsins from cryptophytes. Our results contribute to better understanding of the mechanistic links between the chromophore photochemistry and channel conductance, and provide the basis for using <em>Hc</em>KCR1_C110A as an optogenetic tool.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 5","pages":"Article 168298"},"PeriodicalIF":5.6,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283623004096/pdfft?md5=3a8a45bc7abe3eb13883a1ba081c7f25&pid=1-s2.0-S0022283623004096-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41101891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The UV-A Receptor CRY-DASH1 Up- and Downregulates Proteins Involved in Different Plastidial Pathways UV-A受体CRY-DASH1上调和下调参与不同质体途径的蛋白质。
IF 5.6 2区 生物学
Journal of Molecular Biology Pub Date : 2024-03-01 DOI: 10.1016/j.jmb.2023.168271
Anxhela Rredhi, Jan Petersen, Volker Wagner, Trang Vuong, Wenshuang Li , Wei Li, Laura Schrader, Maria Mittag
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