Journal of Molecular Biology最新文献_第2页

Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging. 用单分子成像技术阐明内在无序蛋白在真核生物转录调控中的作用。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-09 DOI: 10.1016/j.jmb.2025.169343

Shawn Yoshida, Yanghao Zhong, Jonathan Banh, Jiamin Guo, Shasha Chong

{"title":"Elucidating the Roles of Intrinsically Disordered Proteins in Eukaryotic Transcriptional Regulation with Single-Molecule Imaging.","authors":"Shawn Yoshida, Yanghao Zhong, Jonathan Banh, Jiamin Guo, Shasha Chong","doi":"10.1016/j.jmb.2025.169343","DOIUrl":"10.1016/j.jmb.2025.169343","url":null,"abstract":"<p><p>Over 30% of the eukaryotic proteome is comprised of intrinsically disordered protein regions (IDRs) that cannot fold into stable three-dimensional structures. Despite lacking well-defined structures, many IDRs play functional roles in critical cellular processes. One such process is transcription, where many regulatory proteins are intrinsically disordered proteins (IDPs) containing substantial IDRs. Although numerous structured proteins have functions characterized by structural biology approaches, IDRs are less amenable to structure-function relationship characterization using the same methods. Fluorescence microscopy is useful in bridging this gap as it can measure the physical behaviors of IDPs that are important for their functions, e.g., their spatial distribution and diffusion/binding dynamics in the cell. While many fluorescence microscopy methods can serve this purpose, single-molecule imaging methods that enable high spatial and molecular resolution are uniquely capable of accurately characterizing dynamic IDP interactions in transcriptional regulation. In this review, we introduce widely applied single-molecule imaging methods, summarize insights into IDP biology and transcriptional regulation that they have enabled, and discuss their caveats, limitations, and potential directions for innovation.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169343"},"PeriodicalIF":4.7,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615694","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

Properties Governing Native State Entanglements and Relationships to Protein Function 控制天然状态纠缠的特性和与蛋白质功能的关系。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-09 DOI: 10.1016/j.jmb.2025.169342

Justin Petucci , Ian Sitarik , Yang Jiang , Viraj Rana , Hyebin Song , Edward P. O’Brien

{"title":"Properties Governing Native State Entanglements and Relationships to Protein Function","authors":"Justin Petucci , Ian Sitarik , Yang Jiang , Viraj Rana , Hyebin Song , Edward P. O’Brien","doi":"10.1016/j.jmb.2025.169342","DOIUrl":"10.1016/j.jmb.2025.169342","url":null,"abstract":"<div><div>Non-covalent lasso entanglements are structural motifs found in a majority of globular proteins, and their misfolding has been linked to a range of biological consequences. Here, we characterize these motifs’ structural and physicochemical properties, sequence biases, functional site correlations, and universal features across <em>E. coli</em>, <em>S. cerevisiae</em>, and <em>H. sapiens</em>. We find that the crossing residues, which pierce the plane of the entanglement loop, are 11-times more likely to be a β-strand than an α-helix or random coil, and that around this position the protein sequence is 2.5-times more likely to be composed of a stretch of all hydrophobic residues (most often Val, Ile, or Phe) compared to other sequence motifs. Functionally, crossing residues are enriched at enzyme active sites in <em>S. cerevisiae</em> and small molecule binding residues across all species to degrees greater than expected by random chance. Metal binding residues are enriched in these entanglements in <em>H. sapiens.</em> Increasing statistical power by pooling together these species data, we find RNA-binding residues are enriched in these entanglement components. On the other hand, there is a spatial depletion of crossing residues at sites involved in protein binding. Using machine learning, we identified eight robust features predictive of these entanglements, achieving AUROC scores of 0.8 across species. These results are significant because they suggest a direct role for components of native entanglements in particular protein functions, as well as identifying strong secondary structure and sequence preferences in native entanglements.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 19","pages":"Article 169342"},"PeriodicalIF":4.7,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615695","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

Structure of the C-terminal of Viral Responsive Protein 15 (VRP15): A Key Protein During White Spot Syndrome Virus (WSSV) Infection 病毒应答蛋白15 (VRP15) c端结构：白斑综合征病毒（WSSV）感染过程中的关键蛋白

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-08 DOI: 10.1016/j.jmb.2025.169329

Pasunee Laohawutthichai , Sun-Yong Kim , Min Fey Chek , Thapanan Jatuyosporn , Anchalee Tassanakajon , Kuakarun Krusong , Toshio Hakoshima

引用次数: 0

Deciphering Allosteric Disease Mutations Through Intrinsic Dynamics. 通过内在动力学解读变构性疾病突变。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-04 DOI: 10.1016/j.jmb.2025.169326

Berat Kaskaloglu, Ozge Duman, Yigit Kutlu, Turkan Haliloglu

{"title":"Deciphering Allosteric Disease Mutations Through Intrinsic Dynamics.","authors":"Berat Kaskaloglu, Ozge Duman, Yigit Kutlu, Turkan Haliloglu","doi":"10.1016/j.jmb.2025.169326","DOIUrl":"10.1016/j.jmb.2025.169326","url":null,"abstract":"<p><p>Allosteric regulation, driven by conformational and dynamic changes, is fundamental to many biological processes. A major challenge in disease genomics is understanding how specific somatic missense mutations affect protein function, especially when their impact structurally and functionally indirect. In this study, we investigate the link between such mutations and intrinsic protein dynamics, focusing on their allosteric roles. We have analyzed 2549 mutations across 190 human proteins from the ClinVar dataset, using the Gaussian Network Model (GNM) based Transfer Entropy (TE) method. Using the Transient Receptor Potential Mucolipin 1 (TRPML1) channel as a case study, we demonstrate that sequential removal of global modes reveals layered, causal allosteric interactions, where functional sites recur or emerge across various dynamic contexts. Pathogenic mutations significantly coincide with key information sources or sinks within collective information flow. Insights gained from TRPML1 served to inform a large-dataset analysis, providing a topographical view of mutation patterns across a wide range of human proteins and demonstrating broader applicability of this framework Our results provide mechanistic insights into how disease-associated mutations perturb protein dynamics, highlighting distinct components of functional motion and diverse dynamic behaviors offering a path toward allosteric-based interpretation of mutational impact in human disease.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169326"},"PeriodicalIF":4.7,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566913","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

Epistasis in Allosteric Proteins: Can Biophysical Models Provide a Better Framework for Prediction and Understanding? 变构蛋白的上位性：生物物理模型能为预测和理解提供更好的框架吗？

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-04 DOI: 10.1016/j.jmb.2025.169327

David Ross, Drew S Tack, Peter D Tonner, Olga B Vasilyeva

引用次数: 0

Extracellular uncoating of bacteriophage MS2. 噬菌体MS2的细胞外剥离。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-03 DOI: 10.1016/j.jmb.2025.169316

Amelia W Paine, Rees F Garmann, Vinothan N Manoharan

{"title":"Extracellular uncoating of bacteriophage MS2.","authors":"Amelia W Paine, Rees F Garmann, Vinothan N Manoharan","doi":"10.1016/j.jmb.2025.169316","DOIUrl":"10.1016/j.jmb.2025.169316","url":null,"abstract":"<p><p>In the early stages of infection of its host, Escherichia coli, bacteriophage MS2 sheds its icosahedral protein capsid, after which the single-stranded genomic RNA (gRNA) and maturation protein enter the cell as a complex. Although the steps preceding uncoating, which include the binding of the Mat protein to the extracellular filament F-pilus, have been studied in detail, the uncoating step is not well understood. To study when and where uncoating happens, we image the infection process using fluorescence microscopy, separately labelling the MS2 capsid, its gRNA, and the cells. We do two types of experiments. In the first, we incubate the phage in a nonspecific intercalating dye, and we count the number of uncoated and intact phages before and after adding the labeled phages to cells. In the second, we examine the time course of infection by fixing unlabeled samples at different times after adding the phage, and then we label the MS2 gRNA using amplified fluorescence in situ hybridization. In both cases, we find that uncoating can occur anywhere on the F-pili, and that MS2 usually uncoats at a distance from the cell rather than at the cell surface. While these results do not rule out a current hypothesis that virus particles uncoat when the F-pilus retracts and brings them into contact with the cell body, they demonstrate an alternative, extracellular uncoating pathway. We discuss the possiblity that MS2 may have multiple uncoating pathways, and that the rate of each pathway could reflect a trade-off between different risk factors.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169316"},"PeriodicalIF":4.7,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564139","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 Features Within Precursor microRNA-20a Regulate Dicer-TRBP Processing. 前体microRNA-20a的结构特征调控Dicer-TRBP加工。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-01 DOI: 10.1016/j.jmb.2025.169317

Yaping Liu, Cade T Harkner, Megan N Westwood, Aldrex Munsayac, Sarah C Keane

{"title":"Structural Features Within Precursor microRNA-20a Regulate Dicer-TRBP Processing.","authors":"Yaping Liu, Cade T Harkner, Megan N Westwood, Aldrex Munsayac, Sarah C Keane","doi":"10.1016/j.jmb.2025.169317","DOIUrl":"10.1016/j.jmb.2025.169317","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression of target messenger (m) RNAs. To maintain proper miRNA expression levels, the enzymatic processing of primary and precursor miRNA elements must be strictly controlled. However, the molecular determinants underlying this strict regulation of miRNA biogenesis are not fully understood. Here, we determined the solution structure of pre-miR-20a, an oncogenic miRNA and component of the oncomiR-1 cluster, using nuclear magnetic spectroscopy (NMR) spectroscopy and small angle X-ray scattering (SAXS). Our structural studies informed on key secondary structure elements of pre-miR-20a which may control its enzymatic processing, namely a flexible apical loop and single-nucleotide bulge near the dicing site. We found that alternative conformations within pre-miR-20a's apical loop function to self-regulate its Dicer-TRBP processing, and that a single nucleotide bulge at the -5 position from the 5'-cleavage site is critical for efficient processing. We additionally found that a disease-related single-nucleotide polymorphism in pre-miR-20a, predicted to disrupt the structure near the dicing site, resulted in reduced processing. These results further our structural understanding of the oncomiR-1 cluster and show how transient RNA conformers can function to self-regulate maturation.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169317"},"PeriodicalIF":4.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558710","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

Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling. 变构抗体对EGFR活性的调节：桥接实验和计算机模拟。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-01 DOI: 10.1016/j.jmb.2025.169315

Léxane Fournier, Stefan Becker, Stefan Zielonka, Enrico Guarnera

{"title":"Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling.","authors":"Léxane Fournier, Stefan Becker, Stefan Zielonka, Enrico Guarnera","doi":"10.1016/j.jmb.2025.169315","DOIUrl":"10.1016/j.jmb.2025.169315","url":null,"abstract":"<p><p>Allosteric regulation provides a powerful framework for modulating receptor signaling in both physiological and therapeutic contexts. The epidermal growth factor receptor (EGFR), a receptor tyrosine kinase frequently dysregulated in cancer, undergoes activation through conformational transitions that couple extracellular ligand binding to intracellular kinase signaling. Here, we explore how camelid derived VHH (variable domain of the heavy chain of a heavy chain-only)-antibodies can exploit this allosteric architecture to inhibit EGFR function. Using a panel of single domain monospecific and biparatopic antibodies, targeting non-overlapping EGFR epitopes, we combined experimental assays with structure-based modeling to dissect their effects on EGFR signaling and internalization. AlphaFold3-predicted EGFR-antibody complexes were analyzed using the Structure-Based Statistical Mechanical Model of Allostery (SBSMMA) to compute residue-level allosteric modulations induced upon binding. The resulting profiles revealed that only a subset of epitope combinations produced long-range allosteric responses reaching the juxtamembrane segment and the kinase domain. These patterns correlated with effective inhibition of downstream ERK and AKT signaling in cellular assays. In contrast, some constructs with high internalization capacity induced minimal allosteric propagation and weak signaling suppression, indicating a mechanistic decoupling of receptor uptake from conformational regulation. Together, these results define distinct allosteric modes of EGFR modulation by VHH-antibodies and show how computational modeling based on energetic propagation can complement experimental screening to guide the design of next-generation allosteric biologics.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169315"},"PeriodicalIF":4.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558708","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

Nucleocytoplasmic HDAC Inhibition Drives Acetylation-dependent TDP-43 Mislocalization and Disulfide-linked Oligomerization 核细胞质HDAC抑制驱动乙酰化依赖的TDP-43错定位和二硫连接的寡聚化。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-07-01 DOI: 10.1016/j.jmb.2025.169318

Nataliia Lukianenko , Dong Min Kang , Aybuke Bekci , Yun Kyung Kim , Sungsu Lim

{"title":"Nucleocytoplasmic HDAC Inhibition Drives Acetylation-dependent TDP-43 Mislocalization and Disulfide-linked Oligomerization","authors":"Nataliia Lukianenko , Dong Min Kang , Aybuke Bekci , Yun Kyung Kim , Sungsu Lim","doi":"10.1016/j.jmb.2025.169318","DOIUrl":"10.1016/j.jmb.2025.169318","url":null,"abstract":"<div><div>TDP-43 proteinopathies, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), are characterized by aberrant cytoplasmic mislocalization and aggregation of TDP-43. Here, we established a live-cell TDP43-BiFC model to visualize TDP-43 oligomerization in real time and screened diverse cellular stressors. Histone deacetylase (HDAC) inhibition emerged as the most potent trigger of TDP-43 oligomerization. In particular, selective inhibition of the shuttling HDAC4/5 with LMK-235 induced an early and robust formation of cytoplasmic TDP-43 oligomers, comparable to or even exceeding the effect of the pan-HDAC inhibitor apicidin. In contrast, nuclear-restricted HDAC1/3 inhibition by MS-275 prolonged TDP-43 retention in the nucleus with minimal cytoplasmic mislocalization or oligomerization, underscoring distinct roles for nuclear versus nucleocytoplasmic HDACs. Inhibition of cytoplasmic HDAC6 (tubastatin A) had no significant effect. Notably, both shuttling and pan-HDAC inhibition increased TDP-43 acetylation and promoted the accumulation of stable, disulfide-linked TDP-43 oligomers. These findings identify lysine acetylation as a key regulator of disulfide bond-dependent TDP-43 oligomerization and suggest that targeting nucleocytoplasmic HDACs could be a novel therapeutic strategy in TDP-43 proteinopathies.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 19","pages":"Article 169318"},"PeriodicalIF":4.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558709","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

Chaperone Activity of SARS-CoV-2 Nucleocapsid Protein: RNA Annealing and Destabilization Mechanisms SARS-CoV-2核衣壳蛋白的伴侣活性：RNA退火和不稳定机制。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-06-30 DOI: 10.1016/j.jmb.2025.169312

Loussine Zargarian , Xia Ai , Ze-Yu Song , Lara Perez-Gorgol , Esteban Couprie-Diaz , Philippe Fossé , Xu-Guang Xi , Olivier Mauffret

{"title":"Chaperone Activity of SARS-CoV-2 Nucleocapsid Protein: RNA Annealing and Destabilization Mechanisms","authors":"Loussine Zargarian , Xia Ai , Ze-Yu Song , Lara Perez-Gorgol , Esteban Couprie-Diaz , Philippe Fossé , Xu-Guang Xi , Olivier Mauffret","doi":"10.1016/j.jmb.2025.169312","DOIUrl":"10.1016/j.jmb.2025.169312","url":null,"abstract":"<div><div>The recent global COVID-19 pandemic has prompted new research in coronaviruses. Despite the discovery of effective vaccines and therapeutic interventions, coronaviruses remain a threat to humans as the emergence of novel variants or new pathogenic coronaviruses is possible. The N protein or nucleocapsid protein, belonging to the virus’ essential proteins, is mainly involved in the compaction and protection of the viral genome. Here, we show that the SARS-CoV-2 N protein is a very efficient chaperone protein of nucleic acids that aggregates nucleic acids and anneals well-folded and complementary oligonucleotides hairpins <em>in vitro</em>. Using fluorescence and gel shift electrophoresis methods, we showed the high ability of the protein to destabilize nucleic acid secondary structure and to anneal nucleic acid strands. This last activity needs the full-length protein as we demonstrate that protein fragments, while they could display some activities, are considerably less efficient. However, the ability of the full-length protein to destabilize small double-stranded RNAs is poor. Our results show that the N protein possesses a chaperone activity similar to the HIV-1 NCp7 and NCp9 nucleocapsid proteins known as powerful nucleic acid chaperons.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 19","pages":"Article 169312"},"PeriodicalIF":4.7,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551586","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