Journal of Molecular Biology最新文献_第3页

GRAMMCell: Docking-based Cell Modeling Resource.

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-12 DOI: 10.1016/j.jmb.2025.169085

Amar Singh, Andrii M Tytarenko, Vineeth Kumar Ambati, Matthew M Copeland, Petras J Kundrotas, Pavlo O Kasyanov, Eugene A Feinberg, Ilya A Vakser

{"title":"GRAMMCell: Docking-based Cell Modeling Resource.","authors":"Amar Singh, Andrii M Tytarenko, Vineeth Kumar Ambati, Matthew M Copeland, Petras J Kundrotas, Pavlo O Kasyanov, Eugene A Feinberg, Ilya A Vakser","doi":"10.1016/j.jmb.2025.169085","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169085","url":null,"abstract":"<p><p>The environment inside biological cells is densely populated by macromolecules and other cellular components. The crowding has a significant impact on folding and stability of macromolecules, and on kinetics of molecular interactions. Computational approaches to cell modeling, such as molecular dynamics, provide details of macromolecular behavior in concentrated solutions. However, such simulations are either slow, when carried out at atomic resolution, or significantly coarse-grained. Protein docking has been widely used for predicting structures of protein complexes. Systematic docking approaches, such as those based on Fast Fourier Transform (FFT), map the entire intermolecular energy landscape by determining the position and depth of the energy minima. The GRAMMCell web server implements docking-based approach for simulating cell crowded environment by sampling the intermolecular energy landscape generated by GRAMM (Global RAnge Molecular Matching). GRAMM systematically maps the landscape by a spectrum of docking poses corresponding to stable (deep energy minima) and transient (shallow minima) protein interactions. The sampling of these energy landscapes of a large system of proteins is performed in GRAMMCell using highly optimized Markov Chain Monte Carlo protocol. The procedure allows simulation of extra-long trajectories of large, crowded protein systems with atomic resolution accuracy. GRAMMCell is available at https://grammcell.compbio.ku.edu.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169085"},"PeriodicalIF":4.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707995","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

From embryos to condensates: A developmental biologist's journey. 杰拉尔丁-赛杜

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-12 DOI: 10.1016/j.jmb.2025.169083

Geraldine Seydoux

引用次数: 0

A (Scientific) Lifetime Affair With Nucleic Acids.

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-12 DOI: 10.1016/j.jmb.2025.169088

Juli Feigon

{"title":"A (Scientific) Lifetime Affair With Nucleic Acids.","authors":"Juli Feigon","doi":"10.1016/j.jmb.2025.169088","DOIUrl":"10.1016/j.jmb.2025.169088","url":null,"abstract":"<p><p>I am Distinguished Professor in the Chemistry and Biochemistry Department at University of California, Los Angeles, where I was hired in 1985 as the first female assistant professor in the department. I received my PhD from University of California, San Diego, under the guidance of Professor David Kearns, where I used NMR spectroscopy to study drug binding to random sequence DNA and published the first two-dimensional NMR spectra of short synthetic DNA duplexes. From 1982 to 1985 I was a Damon Runyon-Walter Winchell Postdoctoral fellow in the Professor Alexander Rich laboratory, where I investigated structures of Z-DNA by NMR. At UCLA, my lab pioneered the application of macromolecular NMR spectroscopy to the study of DNA and RNA structure, folding, and interactions with cations, drugs, and proteins. We published the first NMR structures of DNA triplexes, quadruplexes, and aptamers, and our work has provided fundamental insights into DNA A-tract bending, cation interactions with DNA, Hoogsteen base pairs, and drug binding to DNA. My lab has made major contributions to understanding RNA folding, dynamics, and function, including pseudoknots, aptamers, ribozymes, and riboswitches, and recognition of RNA by proteins. Over the past 2 decades, the Feigon laboratory pioneered structure-function studies of telomerase, from solution NMR and X-ray crystal structures and dynamics studies of RNA and RNA-protein domains of human and Tetrahymena telomerase, to the first structure of a telomerase holoenzyme, by negative stain EM in 2013, and subsequent cryo-EM structures of telomerase and associated proteins. Recent work also includes structural biology of 7SK RNP.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169088"},"PeriodicalIF":4.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630087","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

Peering into the Bacterial Cell: From Transcription to Functional Genomics.

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-11 DOI: 10.1016/j.jmb.2025.169087

Carol A Gross

引用次数: 0

Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis.

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-10 DOI: 10.1016/j.jmb.2025.169047

Takeshi Chujo, Kazuhito Tomizawa

{"title":"Neurological Diseases Caused by Loss of Transfer RNA Modifications: Commonalities in Their Molecular Pathogenesis.","authors":"Takeshi Chujo, Kazuhito Tomizawa","doi":"10.1016/j.jmb.2025.169047","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169047","url":null,"abstract":"<p><p>Human transfer RNA (tRNA) contains 46 post-transcriptional modifications at specific tRNA positions, which are incorporated by specific modifying enzymes. These tRNA modifications support the structural and biochemical stability of tRNAs and codon-anticodon interactions. Pathogenic genetic variants and disease-associated expressional aberrations have been identified in more than 50 human tRNA modification enzymes and their partner proteins. These are the causes of various diseases and disorders collectively termed 'tRNA modopathies.' Nervous tissue is the most affected tissue in the body upon loss of tRNA modifications, and 37 tRNA modification writers have pathogenic variants that cause neurological diseases. Here, we describe the molecular functions of human tRNA modifications and provide a thorough compilation of >80 human tRNA modification writers and neurological tRNA modopathies. Although largely unexplored, there is growing evidence for the pathogenic mechanisms of neurological tRNA modopathies. Loss of tRNA modifications can cause tRNA destabilization, altered decoding, or production of toxic tRNA fragments, which lead to the severely dysregulated proteostasis that causes neurodegeneration, or the mild translational defects that cause memory impairment. We present herein an overview of these mechanisms and discuss the development of therapeutic strategies and future avenues of research to determine the exact role of tRNA modifications in the nervous system.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169047"},"PeriodicalIF":4.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603139","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

Dynamic Coupling and Entropy Changes in KRAS G12D Mutation: Insights into Molecular Flexibility, Allostery and Function.

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-08 DOI: 10.1016/j.jmb.2025.169075

Aysima Hacisuleyman, Deniz Yuret, Burak Erman

{"title":"Dynamic Coupling and Entropy Changes in KRAS G12D Mutation: Insights into Molecular Flexibility, Allostery and Function.","authors":"Aysima Hacisuleyman, Deniz Yuret, Burak Erman","doi":"10.1016/j.jmb.2025.169075","DOIUrl":"10.1016/j.jmb.2025.169075","url":null,"abstract":"<p><p>The oncogenic G12D mutation in KRAS is a major driver of cancer progression, yet the complete mechanism by which this mutation alters protein dynamics and function remains incompletely understood. Here, we investigate how the G12D mutation alters KRAS's conformational landscape and residue-residue interactions using molecular dynamics simulations coupled with entropy calculations and mutual information (MI) analysis. We demonstrate that the mutation increases local entropy at key functional residues (D12, Y32, G60, and Q61), and introduces new peaks to the Ramachandran angles, disrupting the precise structural alignment necessary for GTP hydrolysis. Notably, while individual residue entropy increases, joint entropy analysis shows a complex reorganization pattern. MI analysis identifies enhanced dynamic coupling between distant residues, suggesting that the mutation establishes new long-range interactions that stabilize the active state. These findings show how G12D mutation redefines KRAS's dynamic network, leading to persistent activation through enhanced residue coupling rather than mere local disruption. Our results suggest novel therapeutic strategies focused on modulating protein dynamics rather than targeting specific binding sites, potentially offering new approaches to combat KRAS-driven cancers.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169075"},"PeriodicalIF":4.7,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595957","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

Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-07 DOI: 10.1016/j.jmb.2025.169074

Philip Kauffman , Haoze He , Andreas Kuhn , Ross E. Dalbey

{"title":"Consecutive Steps of Membrane Insertion of the Two-spanning MscL Protein by Insertase YidC","authors":"Philip Kauffman , Haoze He , Andreas Kuhn , Ross E. Dalbey","doi":"10.1016/j.jmb.2025.169074","DOIUrl":"10.1016/j.jmb.2025.169074","url":null,"abstract":"<div><div>A fundamental problem in biology is understanding how membrane proteins are inserted and assembled into their three-dimensional structures. The YidC/Oxa1/Alb3 insertases, found in bacteria, mitochondria, and chloroplasts play crucial roles in membrane protein insertion. In this study, we investigated the YidC-mediated insertion of MscL, a 2-spanning membrane protein by analyzing a series of translational arrested intermediates and probing the interactions with YidC using thio-crosslinking. Our findings reveal that the first TM segment and the second TM segment of MscL interact cotranslationally with the YidC membrane-embedded greasy slide, although in a delayed manner. The translocation of the periplasmic loop in between the two TM segments only occurs after TM2 engages with the greasy slide of YidC, showing that full insertion occurs late during synthesis. Remarkably, TM2 does not displace TM1 from the slide, and the contact is maintained even when the full-length protein emerges from the ribosome. These results demonstrate a well-ordered sequence of events during the membrane insertion of multi-spanning membrane proteins, providing new insights into the mechanistic role of YidC in protein assembly.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 10","pages":"Article 169074"},"PeriodicalIF":4.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584120","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

Rethinking RNA Modifications: Therapeutic Strategies for Targeting Dysregulated RNA.

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-07 DOI: 10.1016/j.jmb.2025.169046

Isobel E Bowles, Esteban A Orellana

{"title":"Rethinking RNA Modifications: Therapeutic Strategies for Targeting Dysregulated RNA.","authors":"Isobel E Bowles, Esteban A Orellana","doi":"10.1016/j.jmb.2025.169046","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169046","url":null,"abstract":"<p><p>The vast array of cellular ribonucleic acid (RNA) modifications hold a crucial role in regulating RNA stability, folding, localization, and the accuracy of translation. Numerous diseases have been associated with mutations found in genes of RNA-modifying enzymes that can lead to truncated or misfolded proteins incapable of modifying their RNA substrates, causing downstream defects. In contrast, dysregulated levels of RNA-modifying enzymes and the resulting changes in RNA modifications on their substrates are increasingly linked to the activation of oncogenic pathways. This phenomenon has been especially studied through the lens of methyltransferases such as METTL1 and METTL3. The field has developed several small molecule inhibitors of RNA-modifying enzymes to mitigate their related diseases, including targeting the upregulation of METTL3 in cancer. However, increasing evidence suggests that RNA-modifying enzymes play essential roles in numerous cellular processes, including the immune response, neural health, and regeneration, among others. This could lead to off-target effects when treating proteins with small molecules, particularly when these enzymes are upregulated. We propose that developing treatments to specifically target the RNA substrates mis-regulated due to abnormal levels of RNA-modifying enzymes responsible for malignant hallmarks may offer an alternative strategy for treating diseases. We review current RNA-targeted therapies and the diseases they target, including advancements in oligonucleotide modalities and small molecules. We also identify gaps in knowledge that need to be addressed to enhance drug development in the epitranscriptome field to use these therapies to target mis-regulated RNA stemming from altered RNA-modifying enzyme levels.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169046"},"PeriodicalIF":4.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584124","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

5-Methyluridine is Ubiquitous in Pseudomonas aeruginosa tRNA and Modulates Antimicrobial Resistance and Virulence.

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-06 DOI: 10.1016/j.jmb.2025.169020

Jurairat Chittrakanwong, Ruixi Chen, Junzhou Wu, Michael S Demott, Jingjing Sun, Kamonwan Phatinuwat, Juthamas Jaroensuk, Sopapan Atichartpongkul, Skorn Mongkolsuk, Thomas Begley, Peter C Dedon, Mayuree Fuangthong

{"title":"5-Methyluridine is Ubiquitous in Pseudomonas aeruginosa tRNA and Modulates Antimicrobial Resistance and Virulence.","authors":"Jurairat Chittrakanwong, Ruixi Chen, Junzhou Wu, Michael S Demott, Jingjing Sun, Kamonwan Phatinuwat, Juthamas Jaroensuk, Sopapan Atichartpongkul, Skorn Mongkolsuk, Thomas Begley, Peter C Dedon, Mayuree Fuangthong","doi":"10.1016/j.jmb.2025.169020","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169020","url":null,"abstract":"<p><p>Building on decades of work in characterizing the dozens of RNA modifications in the microbial epitranscriptome, recent advances in analytical technology and genetics have revealed systems-level functions for many tRNA modifications. The tRNA (uracil-5-)-methyltransferase TrmA and its product, 5-methyl uridine (m<sup>5</sup>U) at position 54 in the T-loop, however, has not been linked to a specific phenotype. Here, we defined the functional and biological roles of TrmA in Pseudomonas aeruginosa (PA14), a major multidrug-resistant pathogen. Surprisingly, though TrmA was found to site-specifically catalyze m<sup>5</sup>U54 on all PA14 tRNAs, loss of TrmA had no effect on the levels of any of 36 tRNA modifications except m<sup>5</sup>U and had minimal effects on multiple phenotypic parameters, including growth rate, morphology, motility, and biofilm formation. However, loss of TrmA conferred a striking polymyxin antibiotic resistance. mRNA and tRNA profiling and proteomics analyses revealed that TrmA regulates the expression of codon-biased gene families at the level of translation, including components of a type III secretion system (T3SS). Loss of TrmA upregulated T3SS, leading to increased macrophage IL-1β in bacterial challenge tests. Altogether, these results revealed novel biological functions of TrmA and its roles in modulating gene expression at multiple levels in P. aeruginosa.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169020"},"PeriodicalIF":4.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584118","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

Yeast Knowledge Graphs Database for Exploring Saccharomyces Cerevisiae and Schizosaccharomyces Pombe

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2025-03-06 DOI: 10.1016/j.jmb.2025.169072

Mani R. Kumar , Karthick Raja Arulprakasam , An-Nikol Kutevska , Marek Mutwil , Guillaume Thibault

{"title":"Yeast Knowledge Graphs Database for Exploring Saccharomyces Cerevisiae and Schizosaccharomyces Pombe","authors":"Mani R. Kumar , Karthick Raja Arulprakasam , An-Nikol Kutevska , Marek Mutwil , Guillaume Thibault","doi":"10.1016/j.jmb.2025.169072","DOIUrl":"10.1016/j.jmb.2025.169072","url":null,"abstract":"<div><div>Biomedical literature contains an extensive wealth of information on gene and protein function across various biological processes and diseases. However, navigating this vast and often restricted-access data can be challenging, making it difficult to extract specific insights efficiently. In this study, we introduce a high-throughput pipeline that leverages OpenAI’s Generative Pre-Trained Transformer Model (GPT) to automate the extraction and analysis of gene function information. We applied this approach to 84,427 publications on <em>Saccharomyces cerevisiae</em> and 6,452 publications on <em>Schizosaccharomyces pombe</em>, identifying 3,432,749 relationships for budding yeast and 421,198 relationships for <em>S. pombe</em>. This resulted in a comprehensive, searchable online Knowledge Graph database, available at <u>yeast.connectome.tools</u> and <u>spombe.connectome.tools</u>, which offers users extensive access to various interactions and pathways. Our analysis underscores the power of integrating artificial intelligence with bioinformatics, as demonstrated through key insights into important nodes like Hsp104 and Atg8 proteins. This work not only facilitates efficient data extraction in yeast research but also presents a scalable model for similar studies in other biological systems.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 10","pages":"Article 169072"},"PeriodicalIF":4.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584126","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