Journal of Molecular Biology最新文献_第3页

Early-stage determinants of T1-S1 conformations in Kv1.3 channels. Kv1.3通道T1-S1构象的早期决定因素。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-10-04 DOI: 10.1016/j.jmb.2025.169474

Liwei Tu, Aaron Sykes, Therese Davis, Sophia Gross, Carol Deutsch

{"title":"Early-stage determinants of T1-S1 conformations in Kv1.3 channels.","authors":"Liwei Tu, Aaron Sykes, Therese Davis, Sophia Gross, Carol Deutsch","doi":"10.1016/j.jmb.2025.169474","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169474","url":null,"abstract":"<p><p>Early-stage biogenesis of voltage-gated potassium channels (Kv) remains remarkably understudied yet is key to defining co- and post-translational acquisition of Kv secondary, tertiary, and quaternary conformations. Thus, we have studied nascent folding events and their determinants in Kv1.3, a tetrameric ion channel highly expressed in nerve and immune cells. We explore how folding of the T1-S1 linker and T1, an intersubunit recognition domain that ensures correct isoform assembly, are modulated by molecular determinants in the Kv subunit. We focus on the highly conserved C-terminal sequence, S0, in the T1-S1 linker. Using pegylation, a mass-tagging strategy, inter- and intrasubunit crosslinking, we define the molecular determinants of T1-S1 linker accessibility and location. Our findings show that i) dynamic protein-lipid and protein-protein linker interfaces exist, ii) the presence of a T1 domain and its conformation (monomer versus tetramer) impact linker properties, iii) helical formation of S0 occurs in early biogenic stages and does not require the presence of membranes, iv) a core recognition domain (T2) increases T1 dimerization efficiency and promotes tetramer formation, and v) as few as 12 native linker residues enable T1 tetramerization. These findings differ from canonical models and suggest that domain plasticity for Kv1.3 contributes to biogenesis and may underlie domain-domain communication in Kv function.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169474"},"PeriodicalIF":4.5,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237898","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

Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects. 逆转录病毒载体技术用于基因治疗：历史、现状和未来展望。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-10-03 DOI: 10.1016/j.jmb.2025.169473

Soumeya Ali Jaballah, Lizna M Ali, Mohammad Abdullah Jehad, Shaima Akhlaq, Tahir A Rizvi, Farah Mustafa

{"title":"Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects.","authors":"Soumeya Ali Jaballah, Lizna M Ali, Mohammad Abdullah Jehad, Shaima Akhlaq, Tahir A Rizvi, Farah Mustafa","doi":"10.1016/j.jmb.2025.169473","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169473","url":null,"abstract":"<p><p>The concept of gene therapy and its practice has been prevalent for over five decades. The first successful retroviral vector-based gene therapy trial took place ∼35 years ago, followed by several setbacks. However, recent years have seen a surge in successes, offering new hope to patients with genetic and other disorders once deemed untreatable. Over the past decade, rapid advancements in molecular biology have led to the development of safer and more effective gene therapy strategies with various gene delivery systems now in use. Among these, viral vectors such as retroviruses, adenoviruses, and adeno-associated viruses are the most widely employed in both research and clinical settings. This is due to their natural efficiency in delivering genetic material into target cells. Among these viral vectors, retroviruses stand out for their unique ability to reverse-transcribe and integrate their genetic material into the host genome, ensuring stable and long-term gene expression. This review highlights advances in retroviral vector development, examining both their therapeutic potential and associated challenges. It also explores strategies for vector production, including transient and stable systems tailored to meet clinical and regulatory demands. Significant progress is discussed in mitigating insertional mutagenesis and vector silencing. As a result, next-generation retroviral vectors with improved safety and efficacy have made it past regulatory-approval and are commercially available. Current innovations include replication-competent, non-integrating, integration-re-targeted, and hybrid CRISPR/Cas-expressing retroviral vectors undergoing pre-clinical and clinical investigations. This reflects a new era in gene therapy, with retroviral vectors reimagined for greater precision, control, and therapeutic impact.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169473"},"PeriodicalIF":4.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231061","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

Dimer Dissociation and Aggregation Hot-spot Exposure Synergistically Accelerate Light Chain Variable Domain Aggregation Associated With AL Amyloidosis 二聚体解离和聚集热点暴露协同加速与AL淀粉样变性相关的轻链可变结构域聚集。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-10-01 DOI: 10.1016/j.jmb.2025.169468

Sarita Puri , Sharvari Palkar , Amit Kumawat , Ishaan Chaudhary , Basudha Patel , V. Vinoth Kumar , Manoj K. Sriramoju , Kanchan Garai , Shang-Te Danny Hsu , Stefano Ricagno

{"title":"Dimer Dissociation and Aggregation Hot-spot Exposure Synergistically Accelerate Light Chain Variable Domain Aggregation Associated With AL Amyloidosis","authors":"Sarita Puri , Sharvari Palkar , Amit Kumawat , Ishaan Chaudhary , Basudha Patel , V. Vinoth Kumar , Manoj K. Sriramoju , Kanchan Garai , Shang-Te Danny Hsu , Stefano Ricagno","doi":"10.1016/j.jmb.2025.169468","DOIUrl":"10.1016/j.jmb.2025.169468","url":null,"abstract":"<div><div>Light chain (AL) amyloidosis is a life-threatening systemic disorder caused by the aggregation and deposition of antibody light chain (LC) fragments in multiple organs, including the heart and kidneys. In this study, we investigated the early events of aggregation of the highly unstable variable domain (VL) from AL55, a known amyloidogenic and cardiotoxic light chain. Our results show that dimer disruption and exposure of aggregation hot spots synergistically accelerate aggregation. At neutral pH, concentration-dependent dimerization reduces aggregation by limiting aggregation-competent monomers. Dilution or lowering the pH disrupts dimerization, exposes aggregation-prone regions (APRs), and accelerates aggregation. In contrast, when APRs are chemically stabilized, the aggregation rate decreases despite high monomer availability. Together, this study establishes that AL55 VL domain aggregation is regulated by dimer dissociation, electrostatic modulation, and formation of an aggregation-competent conformation involving a dynamic N-terminal (residues 5–26) and dimeric interface (residues 38–56) region, ultimately yielding structurally compact and highly stable fibrils.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169468"},"PeriodicalIF":4.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224613","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 Kinase A Phosphorylates a Conformationally High-energy State of Raf Kinase Inhibitory Protein. 蛋白激酶A磷酸化Raf激酶抑制蛋白的构象高能态。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-26 DOI: 10.1016/j.jmb.2025.169466

Cristina Olivieri, Carmen Biancaniello, V S Manu, Matthew Steven Walters, Larry Masterson, Marsha Rich Rosner, Alfonso De Simone, Gianluigi Veglia

{"title":"Protein Kinase A Phosphorylates a Conformationally High-energy State of Raf Kinase Inhibitory Protein.","authors":"Cristina Olivieri, Carmen Biancaniello, V S Manu, Matthew Steven Walters, Larry Masterson, Marsha Rich Rosner, Alfonso De Simone, Gianluigi Veglia","doi":"10.1016/j.jmb.2025.169466","DOIUrl":"10.1016/j.jmb.2025.169466","url":null,"abstract":"<p><p>Protein kinase A (PKA) is found in all mammalian tissues and plays a critical role in mediating many signaling processes. The structure and phosphorylation mechanism of the catalytic subunit of PKA (PKA-C) have been extensively studied in interaction with linear pseudosubstrate inhibitors, peptide substrates, or protein fragments. To date, however, there have been only a few studies examining how PKA recognizes full-length, folded proteins. Here, we utilized solution NMR spectroscopy in combination with replica-averaged restrained molecular dynamics (RARMD) calculations to investigate the interactions between PKA-C and Raf Kinase Inhibitory Protein (RKIP). RKIP is a member of the phosphatidylethanolamine binding protein (PEBP) family, which regulates important kinase pathways such as the Raf/MAPK pathway and the β-adrenergic receptor/cAMP-dependent PKA signaling cascade. The X-ray structure of RKIP reveals a compact fold, with the phosphorylation consensus sequence well-structured and essentially inaccessible to the kinase. Using Carr-Purcell-Meiboom-Gill (CPMG) and chemical exchange saturation transfer (CEST) experiments, we discovered that RKIP undergoes a conformational equilibrium between a compact fold and a more open conformation, where the C-terminal helix splays away from the RKIP core and exposes its phosphorylation sequence, allowing the kinase to bind and phosphorylate this substrate. The dynamic interplay between the kinase and the substrate may represent a common mechanism for kinases to recognizes well-folded substrates.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169466"},"PeriodicalIF":4.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184513","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 Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-¹³C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0. 结合UCBShift 2.0的新型HMBC-CC-HMQC核磁共振配甲基策略

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-26 DOI: 10.1016/j.jmb.2025.169465

Sonja Knödlstorfer, Giorgia Toscano, Aleksandra L Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, Anna Kapitonova, Roman J Lichtenecker, Paul Schanda, Robert Konrat

{"title":"A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-<sup>13</sup>C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.","authors":"Sonja Knödlstorfer, Giorgia Toscano, Aleksandra L Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, Anna Kapitonova, Roman J Lichtenecker, Paul Schanda, Robert Konrat","doi":"10.1016/j.jmb.2025.169465","DOIUrl":"10.1016/j.jmb.2025.169465","url":null,"abstract":"<p><p>In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional <sup>13</sup>C,<sup>2</sup>H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169465"},"PeriodicalIF":4.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184498","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 Ebolavirus Transcription Regulatory Signal Equilibrates Between Two Structural Conformations to Affect VP30 Binding 埃博拉病毒转录调控信号在两种结构构象之间平衡以影响VP30的结合。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-25 DOI: 10.1016/j.jmb.2025.169464

Jerome M. Edwards , Ambar Kachale , Spencer R. McCleery , Gabrielle A. Law , Vivek Patel , Victoria M. D’Souza , Vincent V. Pham

引用次数: 0

Linker Length and Composition within Disordered Binding Motifs Modulates the Avidity and Reversibility of a Multivalent Protein Interaction Switch 无序结合基序内的连接体长度和组成调节多价蛋白相互作用开关的快速性和可逆性。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-25 DOI: 10.1016/j.jmb.2025.169455

Kiran Sankar Chatterjee, Maria A. Martinez-Yamout, H. Jane Dyson, Peter E. Wright

{"title":"Linker Length and Composition within Disordered Binding Motifs Modulates the Avidity and Reversibility of a Multivalent Protein Interaction Switch","authors":"Kiran Sankar Chatterjee, Maria A. Martinez-Yamout, H. Jane Dyson, Peter E. Wright","doi":"10.1016/j.jmb.2025.169455","DOIUrl":"10.1016/j.jmb.2025.169455","url":null,"abstract":"<div><div>Intrinsically disordered proteins that mediate the cellular transcriptional response to hypoxia play important roles in regulating oxygen stress genes. The feedback inhibitor CITED2 operates a unidirectional switch that efficiently terminates the hypoxic response by displacing the C-terminal activation domain of the hypoxia-inducible factor HIF-1α from its complex with the TAZ1 domain of the transcriptional coactivators CBP and p300. Unidirectionality of the switch arises from subtle allosteric conformational changes in TAZ1 and from differences in the strength of thermodynamic coupling between the TAZ1-binding motifs in the multivalent HIF-1α and CITED2 activation domains. To investigate the role of binding cooperativity, we mutated a linker sequence in the HIF-1α activation domain to alter the thermodynamic coupling between its TAZ1-binding motifs. Linker mutations that enhance the affinity of HIF-1α for TAZ1 enable the HIF-1α activation domain to compete more effectively with bound CITED2. The wide range of mutants, which include insertion, deletion, substitution, and scrambling of residues in the linker, provide insights into the molecular basis for the exquisite tuning of the hypoxic switch. The TAZ1 binding affinity and consequent CITED2 competition enhancement depends both on the flexibility of the linker sequence (particularly the presence of glycine residues) and the unfavorable electrostatic interactions of a highly conserved arginine side chain in the center of the linker with an electropositive surface of TAZ1. The conservation of the linker length and sequence in all vertebrates suggests strong evolutionary pressure to tune HIF-1α binding affinity to be sub-optimal, to ensure unidirectionality of the hypoxic switch.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169455"},"PeriodicalIF":4.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181832","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 Role of Conformational Heterogeneity and Juxtamembrane Regions in the Ephrin A1 Interactions With the EphA2 Receptor Ligand-binding Domain 构象异质性和近膜区域在Ephrin A1与EphA2受体配体结合域相互作用中的结构作用。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-23 DOI: 10.1016/j.jmb.2025.169454

Konstantin S. Mineev , Santosh L. Gande , Annika Wenzel , Verena Linhard , Halle Andrews-Clark , Kerstin Witt , Sabine Köster , Marta Segarra , Melanie A. McDowell , Amparo Acker-Palmer , Harald Schwalbe

引用次数: 0

TRIM52 Ubiquitin Ligase Acts as a Key Recognition Component of the Mammalian fMet/N-degron Pathway TRIM52泛素连接酶是哺乳动物fMet/N-degron通路的关键识别组分。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-19 DOI: 10.1016/j.jmb.2025.169453

Dasom Kim , Juhee Park , Sang-Yoon Kim , Jaehwan Sim , Tae Su Choi , Cheol-Sang Hwang

{"title":"TRIM52 Ubiquitin Ligase Acts as a Key Recognition Component of the Mammalian fMet/N-degron Pathway","authors":"Dasom Kim , Juhee Park , Sang-Yoon Kim , Jaehwan Sim , Tae Su Choi , Cheol-Sang Hwang","doi":"10.1016/j.jmb.2025.169453","DOIUrl":"10.1016/j.jmb.2025.169453","url":null,"abstract":"<div><div>Eukaryotic translation can initiate with formylmethionine (fMet), generating N-terminally formylated proteins in mitochondria and, unexpectedly, in the cytosol. However, the specific mechanism for eliminating cytosolic fMet-bearing proteins has remained elusive. Here, we identify the E3 ubiquitin ligase TRIM52 as the key recognition component of the mammalian fMet/N-degron pathway. TRIM52 targets N-terminally formylated proteins, including TPD54 and SPTAN1, for proteasomal degradation. It recognizes the N-terminal fMet through an evolutionarily conserved acidic loop embedded between its bipartite RING domain. Structural modeling and mutagenesis identify Tyr148 in the acidic loop as critical for fMet recognition without intervening E3 ligase activity. TRIM52 depletion stabilizes fMet-bearing proteins, disrupts proteostasis, and induces caspase-3-dependent apoptosis—phenotypes rescued by enhancing deformylation. These findings establish TRIM52 as a dedicated sensor and effector of the mammalian fMet/N-degron pathway, linking N-terminal formylation to proteostasis and cell survival.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169453"},"PeriodicalIF":4.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111697","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

Unraveling the Diversity of RANBP2: Protein Isoforms and Implications for Cellular Function and Human Disease 揭示RANBP2的多样性：蛋白质亚型及其对细胞功能和人类疾病的影响。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-19 DOI: 10.1016/j.jmb.2025.169452

Sophie Desgraupes, Nathalie Arhel

{"title":"Unraveling the Diversity of RANBP2: Protein Isoforms and Implications for Cellular Function and Human Disease","authors":"Sophie Desgraupes, Nathalie Arhel","doi":"10.1016/j.jmb.2025.169452","DOIUrl":"10.1016/j.jmb.2025.169452","url":null,"abstract":"<div><div>RANBP2 (also known as Nup358) is the largest nucleoporin of the nuclear pore complex (NPC), where it constitutes the main component of the cytoplasmic filaments and regulates nucleocytoplasmic transport. In addition to its NPC-associated functions, RANBP2 also localizes in the endoplasmic reticulum (ER) at annulate lamellae (AL), at mitochondria-ER junctions, and at kinetochores during mitosis, where it contributes to multiple cellular processes including metabolism and mitotic progression. Although most studies focus on the canonical full-length protein (∼358 kDa in humans), multiple smaller bands have been detected across species, suggesting the existence of alternative isoforms. Here, we review all predicted and experimentally supported RANBP2 transcript variants, summarize their structural features and discuss their possible origins, including alternative splicing, genomic recombination and proteolysis. We examine how isoform-specific changes, such as loss of the zinc finger domain, Ran-binding domains, E3 SUMO ligase, or the cyclophilin-like domain, could alter RANBP2′s cellular functions. We also consider evidence for cell-type specific and developmentally regulated expression from non-human models, and evaluate the potential relevance of RANBP2 isoforms in viral infections and neurological disease. By compiling genomic, proteomic, and functional data, this review highlights the need for isoform-resolved approaches to fully understand RANBP2 biology and its contribution to human disease.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 24","pages":"Article 169452"},"PeriodicalIF":4.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111684","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