Journal of Molecular Biology最新文献_第5页

An Atypical Mechanism of SUMOylation of Neurofibromin SecPH Domain Provides New Insights into SUMOylation Site Selection 神经纤维瘤蛋白 SecPH 结构域的非典型 SUMO 化机制为 SUMO 化位点选择提供了新的视角。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-30 DOI: 10.1016/j.jmb.2024.168768

{"title":"An Atypical Mechanism of SUMOylation of Neurofibromin SecPH Domain Provides New Insights into SUMOylation Site Selection","authors":"","doi":"10.1016/j.jmb.2024.168768","DOIUrl":"10.1016/j.jmb.2024.168768","url":null,"abstract":"<div><p>Neurofibromin (Nf1) is a giant multidomain protein encoded by the tumour-suppressor gene <em>NF1</em>. <em>NF1</em> is mutated in a common genetic disease, neurofibromatosis type I (NF1), and in various cancers. The protein has a Ras-GAP (GTPase activating protein) activity but is also connected to diverse signalling pathways through its SecPH domain, which interacts with lipids and different protein partners. We previously showed that Nf1 partially colocalized with the ProMyelocytic Leukemia (PML) protein in PML nuclear bodies, hotspots of SUMOylation, thereby suggesting the potential SUMOylation of Nf1. Here, we demonstrate that the full-length isoform 2 and a SecPH fragment of Nf1 are substrates of the SUMO pathway and identify a well-defined SUMOylation profile of SecPH with two main modified lysines. One of these sites, K1731, is highly conserved and surface-exposed. Despite the presence of an inverted SUMO consensus motif surrounding K1731, and a potential SUMO-interacting motif (SIM) within SecPH, we show that neither of these elements is necessary for K1731 SUMOylation, which is also independent of Ubc9 SUMOylation on K14. A 3D model of an interaction between SecPH and Ubc9 centred on K1731, combined with site-directed mutagenesis, identifies specific structural elements of SecPH required for K1731 SUMOylation, some of which are affected in reported <em>NF1</em> pathogenic variants. This work provides a new example of SUMOylation dependent on the tertiary rather than primary protein structure surrounding the modified site, expanding our knowledge of mechanisms governing SUMOylation site selection.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003887/pdfft?md5=9ede31663fa2a8fcc52d7dc5e454c0f0&pid=1-s2.0-S0022283624003887-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102998","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

Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution 以单核苷酸分辨率观察大肠杆菌 tbpA 核糖开关中 5-́ 干环的同源折叠。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-30 DOI: 10.1016/j.jmb.2024.168771

{"title":"Cotranscriptional Folding of a 5′ Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution","authors":"","doi":"10.1016/j.jmb.2024.168771","DOIUrl":"10.1016/j.jmb.2024.168771","url":null,"abstract":"<div><p>Transcription elongation is one of the most important processes in the cell. During RNA polymerase elongation, the folding of nascent transcripts plays crucial roles in the genetic decision. Bacterial riboswitches are prime examples of RNA regulators that control gene expression by altering their structure upon metabolite sensing. It was previously revealed that the thiamin pyrophosphate-sensing <em>tbpA</em> riboswitch in <em>Escherichia coli</em> cotranscriptionally adopts three main structures leading to metabolite sensing. Here, using single-molecule FRET, we characterize the transition in which the first nascent structure, a 5′ stem-loop, is unfolded during transcription elongation to form the ligand-binding competent structure. Our results suggest that the structural transition occurs in a relatively abrupt manner, <em>i.e.</em>, within a 1–2 nucleotide window. Furthermore, a highly dynamic structural exchange is observed, indicating that riboswitch transcripts perform rapid sampling of nascent co-occurring structures. We also observe that the presence of the RNAP stabilizes the 5′ stem-loop along the elongation process, consistent with RNAP interacting with the 5′ stem-loop. Our study emphasizes the role of early folding stem-loop structures in the cotranscriptional formation of complex RNA molecules involved in genetic regulation.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003917/pdfft?md5=4b592b408e4fe1c2e33ab0984a7938a4&pid=1-s2.0-S0022283624003917-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102999","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 the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling 破译蛋白质-DNA相互作用的语言：结合上下文嵌入和多尺度序列建模的深度学习方法

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-29 DOI: 10.1016/j.jmb.2024.168769

{"title":"Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling","authors":"","doi":"10.1016/j.jmb.2024.168769","DOIUrl":"10.1016/j.jmb.2024.168769","url":null,"abstract":"<div><p>Deciphering the mechanisms governing protein-DNA interactions is crucial for understanding key cellular processes and disease pathways. In this work, we present a powerful deep learning approach that significantly advances the computational prediction of DNA-interacting residues from protein sequences.</p><p>Our method leverages the rich contextual representations learned by pre-trained protein language models, such as ProtTrans, to capture intrinsic biochemical properties and sequence motifs indicative of DNA binding sites. We then integrate these contextual embeddings with a multi-window convolutional neural network architecture, which scans across the sequence at varying window sizes to effectively identify both local and global binding patterns.</p><p>Comprehensive evaluation on curated benchmark datasets demonstrates the remarkable performance of our approach, achieving an area under the ROC curve (AUC) of 0.89 – a substantial improvement over previous state-of-the-art sequence-based predictors. This showcases the immense potential of pairing advanced representation learning and deep neural network designs for uncovering the complex syntax governing protein-DNA interactions directly from primary sequences.</p><p>Our work not only provides a robust computational tool for characterizing DNA-binding mechanisms, but also highlights the transformative opportunities at the intersection of language modeling, deep learning, and protein sequence analysis. The publicly available code and data further facilitate broader adoption and continued development of these techniques for accelerating mechanistic insights into vital biological processes and disease pathways.</p><p>In addition, the code and data for this work are available at <span><span>https://github.com/B1607/DIRP</span><svg><path></path></svg></span>.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003899/pdfft?md5=48e8a1f78b82ff4e5d3d37956f6b0f26&pid=1-s2.0-S0022283624003899-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103000","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

Visualizing Viral RNA Packaging Signals in Action 可视化病毒 RNA 包装信号的作用。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-29 DOI: 10.1016/j.jmb.2024.168765

{"title":"Visualizing Viral RNA Packaging Signals in Action","authors":"","doi":"10.1016/j.jmb.2024.168765","DOIUrl":"10.1016/j.jmb.2024.168765","url":null,"abstract":"<div><p>Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5′ two-thirds of the gRNA of Satellite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate formation of its <em>T</em> = 1 virus-like particle (VLP). These contacts explain why natural virions only package their positive-sense genomes. Asymmetric cryo-EM reconstructions of these VLPs suggest that interactions occur between amino acid residues in the N-terminal ends of the CP subunits and the gRNA PS loop sequences. The base-paired stems of PSs also act non-sequence-specifically by electrostatically promoting the assembly of CP trimers. Importantly, alterations in PS-CP affinity result in an asymmetric distribution of bound PSs inside VLPs, with fuller occupation of the higher affinity 5′ PS RNAs around one vertex, decreasing to an RNA-free opposite vertex within the VLP shell. This distribution suggests that gRNA folding regulates cytoplasmic genome extrusion so that the weakly bound 3′ end of the gRNA, containing the RNA polymerase binding site, extrudes first. This probably occurs after cation-loss induced swelling of the CP-shell, weakening contacts between CP subunits. These data reveal for the first time in any virus how differential PS folding propensity and CP affinities support the multiple roles genomes play in virion assembly and infection. The high degree of conservation between the CP fold of STNV-1 and those of the CPs of many other viruses suggests that these aspects of genome function will be widely shared.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003851/pdfft?md5=687bf5ebb394bcf76ef49e5b060c5f72&pid=1-s2.0-S0022283624003851-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103004","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 Enigma of Transcriptional Activation Domains 转录激活域之谜。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-28 DOI: 10.1016/j.jmb.2024.168766

{"title":"The Enigma of Transcriptional Activation Domains","authors":"","doi":"10.1016/j.jmb.2024.168766","DOIUrl":"10.1016/j.jmb.2024.168766","url":null,"abstract":"<div><p>Activation domains (ADs) of eukaryotic gene activators remain enigmatic for decades as short, extremely variable sequences which often are intrinsically disordered in structure and interact with an uncertain number of targets. The general absence of specificity increasingly complicates the utilization of the widely accepted mechanism of AD function by recruitment of coactivators. The long-standing enigma at the heart of molecular biology demands a fundamental rethinking of established concepts. Here, we review the experimental evidence supporting a novel mechanistic model of gene activation, based on ADs functioning via surfactant-like near-stochastic interactions with gene promoter nucleosomes. This new model is consistent with recent information-rich experimental data obtained using high-throughput synthetic biology and bioinformatics analysis methods, including machine learning. We clarify why the conventional biochemical principle of specificity for sequence, structures, and interactions fails to explain activation domain function. This perspective provides connections to the liquid–liquid phase separation model, signifies near-stochastic interactions as fundamental for the biochemical function, and can be generalized to other cellular functions.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103003","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 Essential RNA Regulatory Elements in the West Nile Virus 3′-Terminal Stem Loop 西尼罗河病毒 3'- 末端茎环中重要 RNA 调控元件的结构。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-28 DOI: 10.1016/j.jmb.2024.168767

{"title":"Structure of Essential RNA Regulatory Elements in the West Nile Virus 3′-Terminal Stem Loop","authors":"","doi":"10.1016/j.jmb.2024.168767","DOIUrl":"10.1016/j.jmb.2024.168767","url":null,"abstract":"<div><p>Flaviviruses, such as West Nile and Dengue Virus, pose a significant and growing threat to global health. Central to the flavivirus life cycle are highly structured 5′- and 3′-untranslated regions (UTRs), which harbor conserved <em>cis</em>-acting RNA elements critical for viral replication and host adaptation. Despite their essential roles, detailed molecular insights into these RNA elements have been limited. By employing nuclear magnetic resonance (NMR) spectroscopy in conjunction with SAXS experiments, we determined the three-dimensional structure of the West Nile Virus (WNV) 3′-terminal stem-loop core, a highly conserved element critical for viral genome cyclization and replication. Single nucleotide mutations at several sites within this RNA abolish the ability of the virus to replicate. These critical sites are located within a short 18-nucleotide hairpin stem, a substructure notable for its conformational flexibility, while the adjoining main stem-loop adopts a well-defined extended helix interrupted by three non-Watson-Crick pairs. This study enhances our understanding of several metastable RNA structures that play key roles in regulating the flavivirus lifecycle, and thereby also opens up potential new avenues for the development of antivirals targeting these conserved RNA structures. In particular, the structure we observe suggests that the plastic junction between the small hairpin and the tail of the longer stem-loop could provide a binding pocket for small molecules, for example potentially stabilizing the RNA in a conformation which hinders the conformational rearrangements critical for viral replication.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103002","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

RNA Polymerase II activity control of gene expression and involvement in disease. RNA 聚合酶 II 的活性控制基因表达并参与疾病防治。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-28 DOI: 10.1016/j.jmb.2024.168770

James C Kuldell, Craig D Kaplan

引用次数: 0

Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models 用 AlphaFold 模型弥合蛋白质序列和结构分类之间的差距。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-26 DOI: 10.1016/j.jmb.2024.168764

{"title":"Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models","authors":"","doi":"10.1016/j.jmb.2024.168764","DOIUrl":"10.1016/j.jmb.2024.168764","url":null,"abstract":"<div><p>Classification of protein domains based on homology and structural similarity serves as a fundamental tool to gain biological insights into protein function. Recent advancements in protein structure prediction, exemplified by AlphaFold, have revolutionized the availability of protein structural data. We focus on classifying about 9000 Pfam families into ECOD (Evolutionary Classification of Domains) by using predicted AlphaFold models and the DPAM (Domain Parser for AlphaFold Models) tool. Our results offer insights into their homologous relationships and domain boundaries. More than half of these Pfam families contain DPAM domains that can be confidently assigned to the ECOD hierarchy. Most assigned domains belong to highly populated folds such as Immunoglobulin-like (IgL), Armadillo (ARM), helix-turn-helix (HTH), and Src homology 3 (SH3). A large fraction of DPAM domains, however, cannot be confidently assigned to ECOD homologous groups. These unassigned domains exhibit statistically different characteristics, including shorter average length, fewer secondary structure elements, and more abundant transmembrane segments. They could potentially define novel families remotely related to domains with known structures or novel superfamilies and folds. Manual scrutiny of a subset of these domains revealed an abundance of internal duplications and recurring structural motifs. Exploring sequence and structural features such as disulfide bond patterns, metal-binding sites, and enzyme active sites helped uncover novel structural folds as well as remote evolutionary relationships. By bridging the gap between sequence-based Pfam and structure-based ECOD domain classifications, our study contributes to a more comprehensive understanding of the protein universe by providing structural and functional insights into previously uncharacterized proteins.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142091314","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 the Recognition of GPRC5D by Talquetamab, a Bispecific Antibody for Multiple Myeloma 多发性骨髓瘤双特异性抗体 Talquetamab 识别 GPRC5D 的结构基础。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-22 DOI: 10.1016/j.jmb.2024.168748

{"title":"Structural Basis for the Recognition of GPRC5D by Talquetamab, a Bispecific Antibody for Multiple Myeloma","authors":"","doi":"10.1016/j.jmb.2024.168748","DOIUrl":"10.1016/j.jmb.2024.168748","url":null,"abstract":"<div><p>Multiple myeloma (MM) is a complex hematological malignancy characterized by abnormal antibody production from plasma cells. Despite advances in the treatment, many patients experience disease relapse or become refractory to treatment. G-protein-coupled receptor class C group 5 member D (GPRC5D), an orphan GPCR predominantly expressed in MM cells, is emerging as a promising target for MM immunotherapy. Talquetamab, a Food and Drug Administration-approved T-cell-directing bispecific antibody developed for treatment of MM, targets GPRC5D. Here, we elucidate the structure of GPRC5D complexed with the Fab fragment of talquetamab, using cryo-electron microscopy, providing the basis for recognition of GPRC5D by the bispecific antibody. GPRC5D forms a symmetric homodimer with the interface between transmembrane helix (TM) 4 of one protomer and TM4/5 of the other protomer. A single talquetamab Fab interacts with the GPRC5D dimer with its orientation toward the dimer interface. All six complementarity-determining regions of talquetamab engage with extracellular loops and TM3/5/7. In particular, the side-chain of an arginine residue from the antibody penetrates into a shallow pocket on the extracellular surface of GPRC5D. The structure offers insights for optimizing antibody design against GPRC5D for relapsed or refractory MM therapy.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":null,"pages":null},"PeriodicalIF":4.7,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054559","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

Single Acetylation-mimetic Mutation in TDP-43 Nuclear Localization Signal Disrupts Importin α1/β Signaling TDP-43核定位信号中的单个乙酰化模拟突变会破坏输入蛋白α1/β的信号传导。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-08-22 DOI: 10.1016/j.jmb.2024.168751

引用次数: 0