Journal of Molecular Biology最新文献_第7页

The Developing Retina Undergoes Mitochondrial Remodeling via PINK1/PRKN-dependent Mitophagy 发育中的视网膜通过依赖PINK1/ prkn的线粒体自噬进行线粒体重塑。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-06-03 DOI: 10.1016/j.jmb.2025.169263

Juan Zapata-Muñoz , Juan Ignacio Jiménez-Loygorri , Michael Stumpe , Beatriz Villarejo-Zori , Sandra Alonso-Gil , Petra Terešak , Benan J. Mathai , Ian G Ganley , Anne Simonsen , Jörn Dengjel , Patricia Boya

{"title":"The Developing Retina Undergoes Mitochondrial Remodeling via PINK1/PRKN-dependent Mitophagy","authors":"Juan Zapata-Muñoz , Juan Ignacio Jiménez-Loygorri , Michael Stumpe , Beatriz Villarejo-Zori , Sandra Alonso-Gil , Petra Terešak , Benan J. Mathai , Ian G Ganley , Anne Simonsen , Jörn Dengjel , Patricia Boya","doi":"10.1016/j.jmb.2025.169263","DOIUrl":"10.1016/j.jmb.2025.169263","url":null,"abstract":"<div><div>Mitophagy, the selective degradation of mitochondria, is essential for retinal ganglion cell (RGC) differentiation and retinal homeostasis. However, the specific mitophagy pathways involved and their temporal dynamics during retinal development and maturation remain poorly understood. Using proteomics analysis of isolated mouse retinas across developmental stages and the mitophagy reporter mouse line, <em>mito</em>-QC, we characterized mitophagy throughout retinogenesis. While mitolysosomes were more prevalent in the mature retina, we observed two distinct mitophagy peaks during embryonic development. The first, independent of PTEN-induced kinase 1 (PINK1) activation, was associated with RGCs. The second, PINK1-dependent peak was triggered after an increase in retinal oxidative stress. This PINK1-dependent, oxidative stress-induced mitophagy pathway is conserved in mice and zebrafish, providing the first evidence of programmed, PINK1-dependent mitophagy during development.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 18","pages":"Article 169263"},"PeriodicalIF":4.7,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144232866","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

NAIL-MS Elucidates Crucial tRNA U34 Modifications in Response to Heat Stress across Eukaryotes and Prokaryotes NAIL-MS揭示了真核生物和原核生物在热应激反应中的关键tRNA U34修饰。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-06-02 DOI: 10.1016/j.jmb.2025.169228

Alexandre Magno Vicente , Katarzyna Hencel , Jannick Schicktanz , Christian Hammann , Alper Akay , Stefanie Kaiser

{"title":"NAIL-MS Elucidates Crucial tRNA U34 Modifications in Response to Heat Stress across Eukaryotes and Prokaryotes","authors":"Alexandre Magno Vicente , Katarzyna Hencel , Jannick Schicktanz , Christian Hammann , Alper Akay , Stefanie Kaiser","doi":"10.1016/j.jmb.2025.169228","DOIUrl":"10.1016/j.jmb.2025.169228","url":null,"abstract":"<div><div>Global warming leads to rising temperatures, necessitating organismal adaptation at the cellular level. One potential mechanism for maintaining proteome integrity during stress is the adaptation of tRNA modifications. While tRNA modification reprogramming has been well-studied under chemical stressors, its role in heat stress remains unclear. To address this, we performed a comparative analysis of tRNA modifications in <em>Arabidopsis thaliana</em>, <em>Saccharomyces cerevisiae</em>, <em>Caenorhabditis elegans</em>, <em>Dictyostelium discoideum</em>, and <em>Escherichia coli</em> under heat stress. We assessed the abundance of 30 modified nucleosides using isotope dilution mass spectrometry under control conditions. <em>A. thaliana</em> showed a similar diversity and abundance of tRNA modifications compared to other eukaryotes, suggesting conservation across species. Under heat stress, overall tRNA modification levels were largely stable, with no significant changes in modifications such as dihydrouridine and N4-acetylcytidine. However, one to four modifications per organism were altered, with uridine modifications at position 34 (U34) being the most prominent change. Here, pulse-chase NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) experiments in <em>E. coli</em> and <em>S. cerevisiae</em> revealed that changes in U34 modifications occurred not only in pre-existing tRNAs but also in newly transcribed tRNAs. These results suggest that existing tRNAs adapt as an early response to heat stress, while newly transcribed tRNAs are reprogrammed to ensure long-term survival under prolonged heat. Our findings highlight the potential role of tRNA modification reprogramming in heat stress adaptation.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 16","pages":"Article 169228"},"PeriodicalIF":4.7,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214544","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

A Fluorescent Probe Targeting EGFR for the Stratification of Prostate Cancer Cells 一种靶向EGFR的前列腺癌细胞分层荧光探针。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-06-02 DOI: 10.1016/j.jmb.2025.169261

Xingxing Wang , Peng Liu , Linli Li , Yan Du , Xiaohong Qin , Zhiqun Shang , Li-Zhi Mi

引用次数: 0

Structural Basis of the LARP4-Filamin A Interaction and Competition with Integrin β7 Tails LARP4-Filamin A与整合素β7 Tails相互作用和竞争的结构基础

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-06-02 DOI: 10.1016/j.jmb.2025.169262

Zhenfeng Mao , Yuanyuan Ding , Yirong Liu, Kunrong Mei, Fumihiko Nakamura

{"title":"Structural Basis of the LARP4-Filamin A Interaction and Competition with Integrin β7 Tails","authors":"Zhenfeng Mao , Yuanyuan Ding , Yirong Liu, Kunrong Mei, Fumihiko Nakamura","doi":"10.1016/j.jmb.2025.169262","DOIUrl":"10.1016/j.jmb.2025.169262","url":null,"abstract":"<div><div>Filamin A (FLNA) is an actin cross-linking protein that connects multiple transmembrane receptors and cytosolic signaling proteins to regulate cell shape, motility, and signaling. Our previous report has shown that FLNA interacts directly with the La-related protein 4 (LARP4) and this interaction is essential for cell migration. Here, using the x-ray crystallography and protein–protein interaction studies, we investigated the molecular basis of LARP4 binding to FLNA. We described the high-resolution structure of the FLNA immunoglobulin-like repeat 21 (R21) and its complex with the LARP4 peptide. The FLNA-binding site in LARP4 is localized between Ala269 and Asn281, where it forms an extended β strand that interacts with the cleft formed by β strands C and D of FLNA R21. Consistent with this structure, the A279Cfs*2 mutation found in catalogue of somatic mutations in cancer (COSMIC) database and the experimentally introduced F277A mutation both disrupt LARP4 binding to FLNA. In contrast, the COSMIC-listed N275S mutation alters LARP4 membrane localization without affecting FLNA interaction, suggesting distinct functional outcomes. Cell migration assays showed that LARP4-knockdown cells expressing FLNA-binding-deficient mutants migrated faster than those expressing wild-type LARP4. The LARP4-binding site on FLNA overlaps with the β-integrin tail-binding region, and <em>in vitro</em> assays revealed that LARP4 can compete with integrin β7 tails for FLNA R21 binding. These results suggest that the LARP4–FLNA interaction may regulate cell migration, at least in part, by competing with integrin tails, although this mechanism has yet to be confirmed <em>in vivo</em>.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169262"},"PeriodicalIF":4.7,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223913","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

Human Rhinovirus B14 with Non-functional Drug-binding Pockets Recovers Infectivity through Stereochemically Constrained Mutations that Restore Capsid Flexibility 具有非功能性药物结合口袋的人鼻病毒B14通过立体化学约束突变恢复衣壳灵活性恢复传染性。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-05-30 DOI: 10.1016/j.jmb.2025.169260

Juan Carlos Gil-Redondo, Luis Valiente, Valentín Riomoros-Barahona, Alejandro Valbuena, Mauricio G. Mateu

{"title":"Human Rhinovirus B14 with Non-functional Drug-binding Pockets Recovers Infectivity through Stereochemically Constrained Mutations that Restore Capsid Flexibility","authors":"Juan Carlos Gil-Redondo, Luis Valiente, Valentín Riomoros-Barahona, Alejandro Valbuena, Mauricio G. Mateu","doi":"10.1016/j.jmb.2025.169260","DOIUrl":"10.1016/j.jmb.2025.169260","url":null,"abstract":"<div><div>Human rhinovirus (RV) is one of the most frequent human pathogens. As causative agents of most common colds, RVs originate serious socioeconomic problems, and they are also associated to or exacerbate severe respiratory diseases. No anti-rhinoviral drugs or vaccines are available yet. In this study, amino acid residues that delimit a druggable pocket in the RV capsid were individually replaced by larger residues, which in most cases resulted in impaired virus infectivity. After serial infections of human host cells, the hampered mutant viruses invariably recovered full infectivity. Sequencing of the viral progeny revealed that, contrary to what has been observed when deleterious mutations were introduced in other virus capsid regions, those mutant RVs did not regain infectivity through the fixation of second-site mutations. Instead, infectivity was always recovered through reversion or pseudo-reversion events that replaced the deleterious bulky residue with a smaller residue, even though this strategy required, in some cases, the improbable fixation of two nucleotides in the corresponding codon. All-atom molecular dynamics simulations and determination of mechanical elasticity by atomic force microscopy revealed that the small-to-large, deleterious mutations reduced the capsid conformational flexibility; and the large-to-small, infectivity-restoring (pseudo)reversions led to recovery of the capsid flexibility. The stereochemistry of this druggable hydrophobic pocket in RV appears to be biologically constrained: The deleterious effect of reducing pocket volume and capsid flexibility is reverted during virus propagation only through same-site mutations that restore pocket volume and capsid flexibility. These constraints may help the further development of anti-RV drugs.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169260"},"PeriodicalIF":4.7,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197930","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

Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes Arkadia和Ark2C通过多种E2酶促进底物泛素化。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-05-30 DOI: 10.1016/j.jmb.2025.169259

Claudia Rossig , Andrej Paluda , Rebecca Chen , Adam J. Middleton , Catherine L. Day

{"title":"Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes","authors":"Claudia Rossig , Andrej Paluda , Rebecca Chen , Adam J. Middleton , Catherine L. Day","doi":"10.1016/j.jmb.2025.169259","DOIUrl":"10.1016/j.jmb.2025.169259","url":null,"abstract":"<div><div>Ubiquitylation is a critical post-translational modification that is required for cell vitality. Attachment of ubiquitin is complex, with the fate of ubiquitylated proteins determined by the length of the attached ubiquitin chains and the nature of the linkage used to build the chains. Many E3 ligases attach ubiquitin chains of different types to substrate proteins in a context specific manner, but the molecular details of how E3 ligases specify chains of different types is poorly understood. Arkadia/RNF111 is a large RING E3 ligase that modifies some substrates with degradative ubiquitin chains, while other substrates are modified with non-degradative ubiquitin chains. Here, using Arkadia and the related E3 ligase, Ark2C, we characterize the RING-E2 complexes that promote assembly of ubiquitin chains of distinct linkages. Our structural studies highlight the conserved nature of the RING-E2 interface, while our binding and activity assays reveal several different E2 enzymes that functionally interact with Ark2C and Arkadia. Using Arkadia, substrate ubiquitylation assays reveal differences in the ability for substrates to be modified, with the E2 enzymes Ubc13 and Ube2K requiring addition of a ‘priming’ ubiquitin molecule before subsequent modification can occur. We also show that substrates that bind Arkadia tightly are more extensively modified, and that prior substrate ubiquitylation enhances subsequent modification. While further studies will be required to understand how RING-E2 pairing is modulated in cells, this study advances our understanding of E2 recruitment and chain assembly by Arkadia and provides tools that may help dissect cellular function.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169259"},"PeriodicalIF":4.7,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197929","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

DeepMS: super-fast peptide identification using end-to-end deep learning method DeepMS：使用端到端深度学习方法的超快速肽识别。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-05-29 DOI: 10.1016/j.jmb.2025.169237

Qianzhou Wei , Jiamin Li , Jin Ma , Qing-Yu He, Gong Zhang

{"title":"DeepMS: super-fast peptide identification using end-to-end deep learning method","authors":"Qianzhou Wei , Jiamin Li , Jin Ma , Qing-Yu He, Gong Zhang","doi":"10.1016/j.jmb.2025.169237","DOIUrl":"10.1016/j.jmb.2025.169237","url":null,"abstract":"<div><div>Mass spectrometry (MS) has emerged as a powerful omics analysis technique, particularly in proteomics, where the initial step involves identifying MS spectra as peptide sequences. However, this process often requires substantial computational resources and expertise, taking hours or even days to complete, thereby limiting the widespread adoption of MS-based omics technologies. To overcome this challenge, we have developed DeepMS, a deep learning-based spectra identification algorithm that overcomes the speed limitations of traditional spectra identification methods. We conducted comprehensive benchmark tests, comparing six deep learning algorithms. Based on the results, we selected the VGG16 algorithm as the core model for DeepMS. This algorithm enables super-fast, end-to-end identification of peptide sequences from MS spectra with high accuracy. DeepMS is adaptable to post-translational modifications, enhancing its versatility. In fact, its identification speed surpasses the generation rate of MS spectra, enabling super-fast identification. Furthermore, we demonstrate the practical application of DeepMS in microorganism detection, highlighting its utility in clinical testing. Through the implementation of DeepMS, our aim is to revolutionize the field of MS-based proteomics and facilitate the broader application of omics technologies, opening new avenues for rapid and efficient analysis in various research and clinical domains.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169237"},"PeriodicalIF":4.7,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191337","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

VWA7 – A Putative Human Phosphatidylcholine-specific Phospholipase C VWA7 -一种推定的人类磷脂酰胆碱特异性磷脂酶CA。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-05-29 DOI: 10.1016/j.jmb.2025.169239

Alexander Klipp, Christina Greitens, Jean-Christophe Leroux, Michael Burger

引用次数: 0

BindUP-Alpha: A Webserver for Predicting DNA-and RNA-binding Proteins based on Experimental and Computational Structural Models☆ BindUP-Alpha：一个基于实验和计算结构模型预测DNA和rna结合蛋白的web服务器。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-05-29 DOI: 10.1016/j.jmb.2025.169240

Dina Alexandrovich , Shani Kagan , Yael Mandel-Gutfreund

{"title":"BindUP-Alpha: A Webserver for Predicting DNA-and RNA-binding Proteins based on Experimental and Computational Structural Models☆","authors":"Dina Alexandrovich , Shani Kagan , Yael Mandel-Gutfreund","doi":"10.1016/j.jmb.2025.169240","DOIUrl":"10.1016/j.jmb.2025.169240","url":null,"abstract":"<div><div>Structural data provides important information on the proteins’ function. Recent development of advanced machine learning and artificial intelligence tools, such as AlphaFold, have led to an explosion of predicted protein structures. However, many of the computed protein models contain unstructured and disordered regions, posing challenges in protein function characterization. Here we present BindUP-Alpha, an upgraded webserver for predicting nucleic acid binding proteins. Our structure-based algorithm utilizes the electrostatic features of the protein surface and other physiochemical and structural properties extracted from the protein sequence. Using a Support Vector Machine (SVM) learning approach, BindUP-Alpha successfully predicts DNA- and RNA-binding proteins from both experimentally solved structures and predicted models. In addition, BindUP-Alpha identifies electrostatic patches on the protein’s surface that represent potential nucleic-acid binding interfaces. BindUP-Alpha is freely accessible at <span><span>https://bindup.technion.ac.il</span><svg><path></path></svg></span>, providing interactive three-dimensional visualizations and downloadable text-based results.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169240"},"PeriodicalIF":4.7,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191336","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

Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent Biosensor Design. 揭示构象变化变构控制的多重摄动响应：在荧光生物传感器设计中的应用。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-05-28 DOI: 10.1016/j.jmb.2025.169234

Melike Berksoz, Ali Rana Atilgan, Burak Kocuk, Canan Atilgan

{"title":"Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent Biosensor Design.","authors":"Melike Berksoz, Ali Rana Atilgan, Burak Kocuk, Canan Atilgan","doi":"10.1016/j.jmb.2025.169234","DOIUrl":"10.1016/j.jmb.2025.169234","url":null,"abstract":"<p><p>Proteins exhibit remarkable conformational flexibility, enabling precise functional regulation through allostery. A key application of allostery is in the design of protein-based sensors, which detect environmental changes-such as ligand binding or post-translational modifications-and convert these cues into measurable signals (e.g., fluorescence). Here, we investigate a series of ligand-binding proteins that serve as sensing domains in direct-response fluorescent biosensors, wherein ligand binding enhances fluorescence output. We employ a multiple force application approach which we term Multiply Perturbed Response (MPR) to identify \"hot spot\" residues that drive the conformational transition from an apo (inactive/OFF) to a holo (active/ON) state. We first present two efficient computational approaches to determine residues and forces that maximize the overlap of the observed conformational change. We then determine the overlap maximizer residues for up to five force insertion locations, and we compare them with actual insertion sites used in existing biosensors. Our analysis shows that the allosteric residues identified by MPR coincide with the fluorescent-protein insertion sites that were mapped experimentally through extensive trial-and-error. This work enhances the utility of linear response theory-based methods in uncovering multiple functionally significant regions that trigger a known conformational change. While the validity of the harmonic approximation in anharmonic conformational transitions needs additional validation, MPR gives a good starting point to explore allosteric sites. The approach might prove useful not only in the design of biosensors, but may also find applications in offering physics-based collective variables in mapping conformational transition pathways of proteins.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169234"},"PeriodicalIF":4.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186145","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