Journal of Molecular Biology最新文献_第6页

Structural Basis of Bifunctional CTP/dCTP Synthase 双功能 CTP/dCTP 合成酶的结构基础。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-20 DOI: 10.1016/j.jmb.2024.168750

{"title":"Structural Basis of Bifunctional CTP/dCTP Synthase","authors":"","doi":"10.1016/j.jmb.2024.168750","DOIUrl":"10.1016/j.jmb.2024.168750","url":null,"abstract":"<div><p>The final step in the de novo synthesis of cytidine 5′-triphosphate (CTP) is catalyzed by CTP synthase (CTPS), which can form cytoophidia in all three domains of life. Recently, we have discovered that CTPS binds to ribonucleotides (NTPs) to form filaments, and have successfully resolved the structures of <em>Drosophila melanogaster</em> CTPS bound with NTPs. Previous biochemical studies have shown that CTPS can bind to deoxyribonucleotides (dNTPs) to produce 2′-deoxycytidine-5′-triphosphate (dCTP). However, the structural basis of CTPS binding to dNTPs is still unclear. In this study, we find that <em>Drosophila</em> CTPS can also form filaments with dNTPs. Using cryo-electron microscopy, we are able to resolve the structure of <em>Drosophila melanogaster</em> CTPS bound to dNTPs with a resolution of up to 2.7 Å. By combining these structural findings with biochemical analysis, we compare the binding and reaction characteristics of NTPs and dNTPs with CTPS. Our results indicate that the same enzyme can act bifunctionally as CTP/dCTP synthase <em>in vitro</em>, and provide a structural basis for these activities.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003590/pdfft?md5=facde5468c5aca8bebdc7ca732330449&pid=1-s2.0-S0022283624003590-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034768","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 Assembly of the Inverse Autotransporter Protein YeeJ is Driven by its C-terminal β-strand 反向自转运蛋白 YeeJ 的组装是由其 C 端 β 链驱动的。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-20 DOI: 10.1016/j.jmb.2024.168749

{"title":"The Assembly of the Inverse Autotransporter Protein YeeJ is Driven by its C-terminal β-strand","authors":"","doi":"10.1016/j.jmb.2024.168749","DOIUrl":"10.1016/j.jmb.2024.168749","url":null,"abstract":"<div><p>Autotransporter proteins are bacterial outer membrane proteins that display passenger domains with various functions through a β-barrel shaped translocation domain. YeeJ is an autotransporter protein from <em>E. coli</em> MG1655. In contrast to most other autotransporter proteins, its passenger domain is located at the C-terminus of the translocation domain. Due to this inverted domain organization, YeeJ belongs to autotransporter proteins of type Ve. To investigate the assembly of YeeJ, the fluorescence of a heterologous mCherry passenger domain was measured to quantify its assembly. Based on AlphaFold2 models of 119 sequences similar to YeeJ, a sequence conservation logo for the β<sub>1</sub>- and the β<sub>12</sub>-strand of type Ve autotransporter proteins was generated. Then, the effect of mutations in these strands on the assembly of YeeJ were analyzed. Mutations of the N-terminal aromatic amino acid of the β<sub>1</sub>-strand did not affect the assembly of the translocation domain and the display of the passenger domain. Likewise, exchange of the β<sub>1</sub>-strand with the β<sub>3</sub>-strand did not impair the assembly of the autotransporter fusion protein. Mutation of the C-terminal aromatic amino acid of the β<sub>12</sub>-strand strongly impaired surface display of the mCherry passenger domain. This amino acid has been shown before as an essential feature of the β-signals of classical autotransporter proteins and outer membrane β-barrel proteins in general. We therefore propose that the β<sub>12</sub>-strand of YeeJ acts as its β-signal and that the assembly of the YeeJ β-barrel is driven by its C-terminal β-strand, like in most other autotransporter proteins, despite its inverted domain organization.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003589/pdfft?md5=c00a80bdeabf022eeccde67e03c46bf3&pid=1-s2.0-S0022283624003589-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034769","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

Conserved N-terminal Regulation of the ACA8 Calcium Pump with Two Calmodulin Binding Sites 具有两个钙调蛋白结合位点的 ACA8 钙泵 N 端保守调控。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-20 DOI: 10.1016/j.jmb.2024.168747

{"title":"Conserved N-terminal Regulation of the ACA8 Calcium Pump with Two Calmodulin Binding Sites","authors":"","doi":"10.1016/j.jmb.2024.168747","DOIUrl":"10.1016/j.jmb.2024.168747","url":null,"abstract":"<div><p>The autoinhibited plasma membrane calcium ATPase ACA8 from <em>A. thaliana</em> has an N-terminal autoinhibitory domain. Binding of calcium-loaded calmodulin at two sites located at residues 42–62 and 74–96 relieves autoinhibition of ACA8 activity.</p><p>Through activity studies and a yeast complementation assay we investigated wild-type (WT) and N-terminally truncated ACA8 constructs (Δ20, Δ30, Δ35, Δ37, Δ40, Δ74 and Δ100) to explore the role of conserved motifs in the N-terminal segment preceding the calmodulin binding sites. Furthermore, we purified WT, Δ20- and Δ100-ACA8, tested activity <em>in vitro</em> and performed structural studies of purified Δ20-ACA8 stabilized in a lipid nanodisc to explore the mechanism of autoinhibition.</p><p>We show that an N-terminal segment between residues 20 and 35 including conserved Phe32, upstream of the calmodulin binding sites, is important for autoinhibition and the activation by calmodulin. Cryo-EM structure determination at 3.3 Å resolution of a beryllium fluoride inhibited E2 form, and at low resolution for an E1 state combined with AlphaFold prediction provide a model for autoinhibition, consistent with the mutational studies.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003565/pdfft?md5=b8cc8fcfc2d15016e9e97d1a6090aedc&pid=1-s2.0-S0022283624003565-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015944","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

BR-ChromNet: Banding resolution localization of chromosome structural abnormality with conditional random field BR-ChromNet：利用条件随机场对染色体结构异常进行带状解析定位

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-14 DOI: 10.1016/j.jmb.2024.168733

{"title":"BR-ChromNet: Banding resolution localization of chromosome structural abnormality with conditional random field","authors":"","doi":"10.1016/j.jmb.2024.168733","DOIUrl":"10.1016/j.jmb.2024.168733","url":null,"abstract":"<div><p>Detecting chromosome structural abnormalities in medical genetics is essential for diagnosing genetic disorders and understanding their implications for an individual’s health. However, existing computational methods are formulated as a binary-class classification problem trained only on representations of positive/negative chromosome pairs. This paper introduces an innovative framework for detecting chromosome abnormalities with banding resolution, capable of precisely identifying and masking the specific abnormal regions. We highlight a pixel-level abnormal mapping strategy guided by banding features. This approach integrates data from both the original image and banding characteristics, enhancing the interpretability of prediction results for cytogeneticists. Furthermore, we have implemented an ensemble approach that pairs a discriminator with a conditional random field heatmap generator. This combination significantly reduces the false positive rate in abnormality screening. We benchmarked our proposed framework with state-of-the-art (SOTA) methods in abnormal screening and structural abnormal region segmentation. Our results show cutting-edge effectiveness and greatly reduce the high false positive rate. It also shows superior performance in sensitivity and segmentation accuracy. Being able to identify abnormal regions consistently shows that our model has demonstrated significant clinical utility with high model interpretability. BRChromNet is open-sourced and available at <span><span>https://github.com/frankchen121212/BR-ChromNet</span><svg><path></path></svg></span></p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003425/pdfft?md5=1f8cc93ab57e200eba1557166ba011f2&pid=1-s2.0-S0022283624003425-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915772","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 CDK9-SPT5 Axis in Control of Transcription Elongation by RNAPII. CDK9-SPT5 轴控制 RNAPII 的转录延伸。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-13 DOI: 10.1016/j.jmb.2024.168746

Rui Sun, Robert P Fisher

{"title":"The CDK9-SPT5 Axis in Control of Transcription Elongation by RNAPII.","authors":"Rui Sun, Robert P Fisher","doi":"10.1016/j.jmb.2024.168746","DOIUrl":"10.1016/j.jmb.2024.168746","url":null,"abstract":"<p><p>The RNA polymerase II (RNAPII) transcription cycle is regulated at every stage by a network of cyclin-dependent protein kinases (CDKs) and protein phosphatases. Progression of RNAPII from initiation to termination is marked by changing patterns of phosphorylation on the highly repetitive carboxy-terminal domain (CTD) of RPB1, its largest subunit, suggesting the existence of a CTD code. In parallel, the conserved transcription elongation factor SPT5, large subunit of the DRB sensitivity-inducing factor (DSIF), undergoes spatiotemporally regulated changes in phosphorylation state that may be directly linked to the transitions between transcription-cycle phases. Here we review insights gained from recent structural, biochemical, and genetic analyses of human SPT5, which suggest that two of its phosphorylated regions perform distinct functions at different points in transcription. Phosphorylation within a flexible, RNA-binding linker promotes release from the promoter-proximal pause-frequently a rate-limiting step in gene expression-whereas modifications in a repetitive carboxy-terminal region are thought to favor processive elongation, and are removed just prior to termination. Phosphorylations in both motifs depend on CDK9, catalytic subunit of positive transcription elongation factor b (P-TEFb); their different timing of accumulation on chromatin and function during the transcription cycle might reflect their removal by different phosphatases, different kinetics of phosphorylation by CDK9, or both. Perturbations of SPT5 regulation have profound impacts on viability and development in model organisms through largely unknown mechanisms, while enzymes that modify SPT5 have emerged as potential therapeutic targets in cancer; elucidating a putative SPT5 code is therefore a high priority.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987110","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

Structural Basis for C2′-methoxy Recognition by DNA Polymerases and Function Improvement DNA 聚合酶识别 C2'-methoxy 的结构基础和功能改进。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-13 DOI: 10.1016/j.jmb.2024.168744

引用次数: 0

Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases RNA 靶向 pAgo 核酸酶中不寻常的向导结合袋。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-13 DOI: 10.1016/j.jmb.2024.168745

{"title":"Unusual Guide-binding Pockets in RNA-targeting pAgo Nucleases","authors":"","doi":"10.1016/j.jmb.2024.168745","DOIUrl":"10.1016/j.jmb.2024.168745","url":null,"abstract":"<div><p>Argonaute nucleases use small nucleic acid guides to recognize and degrade complementary nucleic acid targets. Most prokaryotic Argonautes (pAgos) recognize DNA targets and may play a role in cell immunity against invader genetic elements. We have recently described two related groups of pAgo nucleases that have distinct specificity for DNA guides and RNA targets (DNA > RNA pAgos). Here, we describe additional pAgos from the same clades of the pAgo tree and demonstrate that they have the same unusual nucleic acid specificity. The two groups of DNA > RNA pAgos have non-standard guide-binding pockets in the MID domain and differ in the register of guide DNA binding and target cleavage. In contrast to other pAgos, which coordinate the 5′-end of the guide molecule by their C-terminal carboxyl, DNA > RNA pAgos have an extended C-terminus located away from the MID pocket. We show that modifications of the C-terminus do not affect guide DNA binding, but inhibit cleavage of complementary and mismatched RNA targets by some DNA > RNA pAgos. Our data suggest that the unique C-terminus found in DNA > RNA pAgos can modulate their catalytic properties and can be used as a target for pAgo modifications.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987111","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

Multiple Forms and Functions of Premature Termination by RNA Polymerase II. RNA 聚合酶 II 提前终止的多种形式和功能。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-09 DOI: 10.1016/j.jmb.2024.168743

David L Bentley

{"title":"Multiple Forms and Functions of Premature Termination by RNA Polymerase II.","authors":"David L Bentley","doi":"10.1016/j.jmb.2024.168743","DOIUrl":"10.1016/j.jmb.2024.168743","url":null,"abstract":"<p><p>Eukaryotic genomes are widely transcribed by RNA polymerase II (pol II) both within genes and in intergenic regions. POL II elongation complexes comprising the polymerase, the DNA template and nascent RNA transcript must be extremely processive in order to transcribe the longest genes which are over 1 megabase long and take many hours to traverse. Dedicated termination mechanisms are required to disrupt these highly stable complexes. Transcription termination occurs not only at the 3' ends of genes once a full length transcript has been made, but also within genes and in promiscuously transcribed intergenic regions. Termination at these latter positions is termed \"premature\" because it is not triggered in response to a specific signal that marks the 3' end of a gene, like a polyA site. One purpose of premature termination is to remove polymerases from intergenic regions where they are \"not wanted\" because they may interfere with transcription of overlapping genes or the progress of replication forks. Premature termination has recently been appreciated to occur at surprisingly high rates within genes where it is speculated to serve regulatory or quality control functions. In this review I summarize current understanding of the different mechanisms of premature termination and its potential functions.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141911138","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

Protein Misfolding Releases Human HSF1 from HSP70 Latency Control 蛋白质错误折叠会使人类热休克因子 1 (HSF1) 脱离 HSP70 的潜伏控制。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-08 DOI: 10.1016/j.jmb.2024.168740

{"title":"Protein Misfolding Releases Human HSF1 from HSP70 Latency Control","authors":"","doi":"10.1016/j.jmb.2024.168740","DOIUrl":"10.1016/j.jmb.2024.168740","url":null,"abstract":"<div><p>Heat shock factor 1 (HSF1) responds to stress to mount the heat shock response (HSR), a conserved transcriptional program that allows cells to maintain proteostasis by upregulating heat shock proteins (HSPs). The homeostatic stress regulation of HSF1 plays a key role in human physiology and health but its mechanism has remained difficult to pinpoint. Recent work in the budding yeast model has implicated stress-inducible chaperones of the HSP70 family as direct negative regulators of HSF1 activity. Here, we have investigated the latency control and activation of human HSF1 by HSP70 and misfolded proteins. Purified oligomeric HSF1-HSP70 (HSPA1A) complexes exhibited basal DNA binding activity that was inhibited by increasing the levels of HSP70 and, importantly, misfolded proteins reverted the inhibitory effect. Using site-specific UV photo-crosslinking, we monitored HSP70-HSF1 complexes in HEK293T cells. While HSF1 was bound by the substrate binding domain of HSP70 in unstressed cells, activation of HSF1 by heat shock as well as by inducing the misfolding of newly synthesized proteins resulted in release of HSF1 from the chaperone. Taken our results together, we conclude that latent HSF1 populate dynamic complexes with HSP70, which are sensitive to increased levels of misfolded proteins that compete for binding to the HSP70 substrate binding domain. Thus, human HSF1 is activated by various stress conditions that all titrate available HSP70.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003498/pdfft?md5=efcc960570a124c7e6a17c6d1c255cd6&pid=1-s2.0-S0022283624003498-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141911171","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

IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy. IIFS2.0：基于缓存策略的蛋白质序列处理增量特征选择改进方法

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-08 DOI: 10.1016/j.jmb.2024.168741

Chaolu Meng, Yue Pei, Yongbo Bu, Qing Liu, Qun Li, Quan Zou, Ying Zhang

{"title":"IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy.","authors":"Chaolu Meng, Yue Pei, Yongbo Bu, Qing Liu, Qun Li, Quan Zou, Ying Zhang","doi":"10.1016/j.jmb.2024.168741","DOIUrl":"10.1016/j.jmb.2024.168741","url":null,"abstract":"<p><p>The purpose of feature selection in protein sequence recognition problems is to select the optimal feature set and use it as training input for classifiers and discover key sequence features of specific proteins. In the feature selection process, relevant features associated with the target task will be retained, and irrelevant and redundant features will be removed. Therefore, in an ideal state, a feature combination with smaller feature dimensions and higher performance indicators is desired. This paper proposes an algorithm called IIFS2.0 based on the cache elimination strategy, which takes the local optimal combination of cached feature subsets as a breakthrough point. It searches for a new feature combination method through the cache elimination strategy to avoid the drawbacks of human factors and excessive reliance on feature sorting results. We validated and analyzed its effectiveness on the protein dataset, demonstrating that IIFS2.0 significantly reduces the dimensionality of feature combinations while also improving various evaluation indicators. In addition, we provide IIFS2.0 on https://112.124.26.17:8006/ for researchers to use.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141911137","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